From 61406f5f9dd97d125fff7cd1bf94586f96011744 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Wed, 29 Nov 2023 09:36:04 -0800 Subject: [PATCH 01/25] adding chewbbaca/createschema module --- .../nf-core/chewbbaca/createschema/main.nf | 67 ++++++++ .../nf-core/chewbbaca/createschema/meta.yml | 57 +++++++ tests/config/pytest_modules.yml | 4 + .../nf-core/chewbbaca/createschema/main.nf | 28 ++++ .../chewbbaca/createschema/nextflow.config | 5 + .../nf-core/chewbbaca/createschema/test.yml | 157 ++++++++++++++++++ 6 files changed, 318 insertions(+) create mode 100644 modules/nf-core/chewbbaca/createschema/main.nf create mode 100644 modules/nf-core/chewbbaca/createschema/meta.yml create mode 100644 tests/modules/nf-core/chewbbaca/createschema/main.nf create mode 100644 tests/modules/nf-core/chewbbaca/createschema/nextflow.config create mode 100644 tests/modules/nf-core/chewbbaca/createschema/test.yml diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf new file mode 100644 index 00000000000..71df5ea27eb --- /dev/null +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -0,0 +1,67 @@ +process CHEWBBACA_CREATESCHEMA { + tag "$meta.id" + label 'process_low' + + conda "bioconda::chewbbaca=3.3.1" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/chewbbaca:3.3.1--pyhdfd78af_0': + 'biocontainers/chewbbaca:3.3.1--pyhdfd78af_0' }" + + input: + tuple val(meta), path(fasta, stageAs: "input_genomes/*") + path prodigal_tf + path cds + + + output: + path 'results/*' , emit: schema + path "results/cds_coordinates.tsv" , emit: cds_coordinates + path "results/invalid_cds.txt" , emit: invalid_cds + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def schema = "--n ${prefix}" + def prodigal_tf = prodigal_tf ? "--ptf ${prodigal_tf}" : "" + def cds = cds ? "--cds ${cds}" : "" + + """ + + + chewie \\ + CreateSchema \\ + -i input_genomes/ \\ + -o results \\ + $schema \\ + $args \\ + $prodigal_tf \\ + $cds \\ + --cpu $task.cpus + + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + chewbbaca: \$(echo \$(chewie --version 2>&1 | sed 's/^.*chewBBACA version: //g; s/Using.*\$//' )) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def schema = "--n ${prefix}" + + + """ + mkdir -p results/$schema + + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + chewbbaca: \$(echo \$(chewie --version 2>&1 | sed 's/^.*chewBBACA version: //g; s/Using.*\$//' )) + END_VERSIONS + """ +} diff --git a/modules/nf-core/chewbbaca/createschema/meta.yml b/modules/nf-core/chewbbaca/createschema/meta.yml new file mode 100644 index 00000000000..6e2006a99cb --- /dev/null +++ b/modules/nf-core/chewbbaca/createschema/meta.yml @@ -0,0 +1,57 @@ +--- +name: "chewbbaca_createschema" +description: write your description here +keywords: + - cgMLST + - WGS + - genomics +tools: + - "chewbbaca": + description: "A complete suite for gene-by-gene schema creation and strain identification." + homepage: "https://chewbbaca.readthedocs.io/en/latest/index.html" + documentation: "https://chewbbaca.readthedocs.io/en/latest/index.html" + tool_dev_url: "https://github.com/B-UMMI/chewBBACA" + doi: "10.1099/mgen.0.000166" + licence: ["GPL v3"] + +## TODO nf-core: Add a description of all of the variables used as input +input: + # Only when we have meta + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + + - fasta: + type: directory + description: One or multiple FASTA files to create schema from + pattern: "*.{fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz}" + + - prodigal_tf: + type: file + description: File containing the prodigal training file + pattern: "*.ptf" + + - cds: + type: file + description: File containing the prodigal cds file + pattern: "*.cds" + + +## TODO nf-core: Add a description of all of the variables used as output +output: + + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + + - schema_dir: + type: directory + description: schema directory + pattern: "*/" + + +authors: + - "@anwarMZ" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 43f572eca56..eac90ed74fb 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -615,6 +615,10 @@ checkv/updatedatabase: - modules/nf-core/checkv/updatedatabase/** - tests/modules/nf-core/checkv/updatedatabase/** +chewbbaca/createschema: + - modules/nf-core/chewbbaca/createschema/** + - tests/modules/nf-core/chewbbaca/createschema/** + chromap/chromap: - modules/nf-core/chromap/chromap/** - tests/modules/nf-core/chromap/chromap/** diff --git a/tests/modules/nf-core/chewbbaca/createschema/main.nf b/tests/modules/nf-core/chewbbaca/createschema/main.nf new file mode 100644 index 00000000000..33cf31aea04 --- /dev/null +++ b/tests/modules/nf-core/chewbbaca/createschema/main.nf @@ -0,0 +1,28 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { CHEWBBACA_CREATESCHEMA } from '../../../../../modules/nf-core/chewbbaca/createschema/main.nf' + +workflow test_chewbbaca_createschema { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)] + ptf = [] + cds = [] + + CHEWBBACA_CREATESCHEMA ( input, ptf, cds) +} + +workflow test_chewbbaca_createschema_multi { + + input = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] ] + ptf = [] + cds = [] + + CHEWBBACA_CREATESCHEMA ( input, ptf, cds) +} diff --git a/tests/modules/nf-core/chewbbaca/createschema/nextflow.config b/tests/modules/nf-core/chewbbaca/createschema/nextflow.config new file mode 100644 index 00000000000..50f50a7a357 --- /dev/null +++ b/tests/modules/nf-core/chewbbaca/createschema/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/nf-core/chewbbaca/createschema/test.yml b/tests/modules/nf-core/chewbbaca/createschema/test.yml new file mode 100644 index 00000000000..88965bd7e23 --- /dev/null +++ b/tests/modules/nf-core/chewbbaca/createschema/test.yml @@ -0,0 +1,157 @@ +- name: chewbbaca createschema test_chewbbaca_createschema + command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema -c ./tests/config/nextflow.config + tags: + - chewbbaca + - chewbbaca/createschema + files: + - path: output/chewbbaca/results/cds_coordinates.tsv + md5sum: 7fef49207aa024b68f465e986f4c7444 + - path: output/chewbbaca/results/invalid_cds.txt + md5sum: d0afbd9996054d8838e62dc3e852fa07 + - path: output/chewbbaca/results/test/.genes_list + contains: + - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ' + - path: output/chewbbaca/results/test/.schema_config + md5sum: 92b512f65fde7dce321ada54e5c431e9 + - path: output/chewbbaca/results/test/contigs-protein1.fasta + md5sum: 79f1e1c7105c0b34195e18c34960d2d4 + - path: output/chewbbaca/results/test/contigs-protein10.fasta + md5sum: 9fd40f7247cb3ed93f66828dbbfbac22 + - path: output/chewbbaca/results/test/contigs-protein11.fasta + md5sum: b2f94d1babce56f5c1e46ccd35d2a7d7 + - path: output/chewbbaca/results/test/contigs-protein13.fasta + md5sum: 7314303d55a8598b229eca32ddeea14d + - path: output/chewbbaca/results/test/contigs-protein14.fasta + md5sum: 2a8023e86fb119834f2d050daee33958 + - path: output/chewbbaca/results/test/contigs-protein16.fasta + md5sum: e006bb0da17f845c1672caed826d4ab7 + - path: output/chewbbaca/results/test/contigs-protein17.fasta + md5sum: 58f2501c0a7e48aaa86a87d01740b5c4 + - path: output/chewbbaca/results/test/contigs-protein18.fasta + md5sum: 6b4f385dc954df1fd2057a1c57872338 + - path: output/chewbbaca/results/test/contigs-protein19.fasta + md5sum: 3614c079d0b08f0c59bdaac9dcea0409 + - path: output/chewbbaca/results/test/contigs-protein2.fasta + md5sum: 0b982a66a0f001f11a86cc1b5a4ef80d + - path: output/chewbbaca/results/test/contigs-protein20.fasta + md5sum: 75b2492e5db0848079faafe6f60fe9fd + - path: output/chewbbaca/results/test/contigs-protein4.fasta + md5sum: 4ce5090bf2547bc588f0f8d00ae4a59d + - path: output/chewbbaca/results/test/contigs-protein6.fasta + md5sum: ffebf19b61285767a14f486af7181c30 + - path: output/chewbbaca/results/test/contigs-protein7.fasta + md5sum: ee06d9303c5b7844b003daa42b7a1869 + - path: output/chewbbaca/results/test/contigs-protein8.fasta + md5sum: 2a00efc36b036ab7f6c30f85533963cf + - path: output/chewbbaca/results/test/contigs-protein9.fasta + md5sum: ad9372b812030db327fa12d1e1731e85 + - path: output/chewbbaca/results/test/short/contigs-protein10_short.fasta + md5sum: 9fd40f7247cb3ed93f66828dbbfbac22 + - path: output/chewbbaca/results/test/short/contigs-protein11_short.fasta + md5sum: b2f94d1babce56f5c1e46ccd35d2a7d7 + - path: output/chewbbaca/results/test/short/contigs-protein13_short.fasta + md5sum: 7314303d55a8598b229eca32ddeea14d + - path: output/chewbbaca/results/test/short/contigs-protein14_short.fasta + md5sum: 2a8023e86fb119834f2d050daee33958 + - path: output/chewbbaca/results/test/short/contigs-protein16_short.fasta + md5sum: e006bb0da17f845c1672caed826d4ab7 + - path: output/chewbbaca/results/test/short/contigs-protein17_short.fasta + md5sum: 58f2501c0a7e48aaa86a87d01740b5c4 + - path: output/chewbbaca/results/test/short/contigs-protein18_short.fasta + md5sum: 6b4f385dc954df1fd2057a1c57872338 + - path: output/chewbbaca/results/test/short/contigs-protein19_short.fasta + md5sum: 3614c079d0b08f0c59bdaac9dcea0409 + - path: output/chewbbaca/results/test/short/contigs-protein1_short.fasta + md5sum: 79f1e1c7105c0b34195e18c34960d2d4 + - path: output/chewbbaca/results/test/short/contigs-protein20_short.fasta + md5sum: 75b2492e5db0848079faafe6f60fe9fd + - path: output/chewbbaca/results/test/short/contigs-protein2_short.fasta + md5sum: 0b982a66a0f001f11a86cc1b5a4ef80d + - path: output/chewbbaca/results/test/short/contigs-protein4_short.fasta + md5sum: 4ce5090bf2547bc588f0f8d00ae4a59d + - path: output/chewbbaca/results/test/short/contigs-protein6_short.fasta + md5sum: ffebf19b61285767a14f486af7181c30 + - path: output/chewbbaca/results/test/short/contigs-protein7_short.fasta + md5sum: ee06d9303c5b7844b003daa42b7a1869 + - path: output/chewbbaca/results/test/short/contigs-protein8_short.fasta + md5sum: 2a00efc36b036ab7f6c30f85533963cf + - path: output/chewbbaca/results/test/short/contigs-protein9_short.fasta + md5sum: ad9372b812030db327fa12d1e1731e85 + - path: output/chewbbaca/versions.yml + +- name: chewbbaca createschema test_chewbbaca_createschema_multi + command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema_multi -c ./tests/config/nextflow.config + tags: + - chewbbaca + - chewbbaca/createschema + files: + - path: output/chewbbaca/results/cds_coordinates.tsv + md5sum: e62f4e808939f97ccdbe4d17c1521b6c + - path: output/chewbbaca/results/invalid_cds.txt + md5sum: d0afbd9996054d8838e62dc3e852fa07 + - path: output/chewbbaca/results/test/.genes_list + contains: + - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ' + - path: output/chewbbaca/results/test/.schema_config + md5sum: 92b512f65fde7dce321ada54e5c431e9 + - path: output/chewbbaca/results/test/contigs-protein1.fasta + md5sum: 79f1e1c7105c0b34195e18c34960d2d4 + - path: output/chewbbaca/results/test/contigs-protein10.fasta + md5sum: 9fd40f7247cb3ed93f66828dbbfbac22 + - path: output/chewbbaca/results/test/contigs-protein14.fasta + md5sum: 2a8023e86fb119834f2d050daee33958 + - path: output/chewbbaca/results/test/contigs-protein16.fasta + md5sum: e006bb0da17f845c1672caed826d4ab7 + - path: output/chewbbaca/results/test/contigs-protein17.fasta + md5sum: 58f2501c0a7e48aaa86a87d01740b5c4 + - path: output/chewbbaca/results/test/contigs-protein18.fasta + md5sum: 6b4f385dc954df1fd2057a1c57872338 + - path: output/chewbbaca/results/test/contigs-protein19.fasta + md5sum: 3614c079d0b08f0c59bdaac9dcea0409 + - path: output/chewbbaca/results/test/contigs-protein2.fasta + md5sum: 0b982a66a0f001f11a86cc1b5a4ef80d + - path: output/chewbbaca/results/test/contigs-protein20.fasta + md5sum: 75b2492e5db0848079faafe6f60fe9fd + - path: output/chewbbaca/results/test/contigs-protein4.fasta + md5sum: 4ce5090bf2547bc588f0f8d00ae4a59d + - path: output/chewbbaca/results/test/contigs-protein6.fasta + md5sum: ffebf19b61285767a14f486af7181c30 + - path: output/chewbbaca/results/test/contigs-protein7.fasta + md5sum: ee06d9303c5b7844b003daa42b7a1869 + - path: output/chewbbaca/results/test/contigs-protein8.fasta + md5sum: 2a00efc36b036ab7f6c30f85533963cf + - path: output/chewbbaca/results/test/contigs-protein9.fasta + md5sum: ad9372b812030db327fa12d1e1731e85 + - path: output/chewbbaca/results/test/genome-protein1.fasta + md5sum: c1b28842a7e89e3bcc7d655afe51c609 + - path: output/chewbbaca/results/test/short/contigs-protein10_short.fasta + md5sum: 9fd40f7247cb3ed93f66828dbbfbac22 + - path: output/chewbbaca/results/test/short/contigs-protein14_short.fasta + md5sum: 2a8023e86fb119834f2d050daee33958 + - path: output/chewbbaca/results/test/short/contigs-protein16_short.fasta + md5sum: e006bb0da17f845c1672caed826d4ab7 + - path: output/chewbbaca/results/test/short/contigs-protein17_short.fasta + md5sum: 58f2501c0a7e48aaa86a87d01740b5c4 + - path: output/chewbbaca/results/test/short/contigs-protein18_short.fasta + md5sum: 6b4f385dc954df1fd2057a1c57872338 + - path: output/chewbbaca/results/test/short/contigs-protein19_short.fasta + md5sum: 3614c079d0b08f0c59bdaac9dcea0409 + - path: output/chewbbaca/results/test/short/contigs-protein1_short.fasta + md5sum: 79f1e1c7105c0b34195e18c34960d2d4 + - path: output/chewbbaca/results/test/short/contigs-protein20_short.fasta + md5sum: 75b2492e5db0848079faafe6f60fe9fd + - path: output/chewbbaca/results/test/short/contigs-protein2_short.fasta + md5sum: 0b982a66a0f001f11a86cc1b5a4ef80d + - path: output/chewbbaca/results/test/short/contigs-protein4_short.fasta + md5sum: 4ce5090bf2547bc588f0f8d00ae4a59d + - path: output/chewbbaca/results/test/short/contigs-protein6_short.fasta + md5sum: ffebf19b61285767a14f486af7181c30 + - path: output/chewbbaca/results/test/short/contigs-protein7_short.fasta + md5sum: ee06d9303c5b7844b003daa42b7a1869 + - path: output/chewbbaca/results/test/short/contigs-protein8_short.fasta + md5sum: 2a00efc36b036ab7f6c30f85533963cf + - path: output/chewbbaca/results/test/short/contigs-protein9_short.fasta + md5sum: ad9372b812030db327fa12d1e1731e85 + - path: output/chewbbaca/results/test/short/genome-protein1_short.fasta + md5sum: c1b28842a7e89e3bcc7d655afe51c609 + - path: output/chewbbaca/versions.yml From 4a7895cd742d40f95574486048f22f872584ec48 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Wed, 29 Nov 2023 10:34:18 -0800 Subject: [PATCH 02/25] updated for handling a mix of uncompressed and compressed files --- .../nf-core/chewbbaca/createschema/main.nf | 2 +- .../nf-core/chewbbaca/createschema/meta.yml | 22 ++++-- .../nf-core/chewbbaca/createschema/main.nf | 12 +++ .../nf-core/chewbbaca/createschema/test.yml | 77 +++++++++++++++++++ 4 files changed, 104 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf index 71df5ea27eb..29f97d0dc71 100644 --- a/modules/nf-core/chewbbaca/createschema/main.nf +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -30,7 +30,7 @@ process CHEWBBACA_CREATESCHEMA { def cds = cds ? "--cds ${cds}" : "" """ - + find ./input_genomes/ -name "*.gz" | sed 's/.gz//' | xargs -I {} bash -c 'gzip -cdf {}.gz > {}' chewie \\ CreateSchema \\ diff --git a/modules/nf-core/chewbbaca/createschema/meta.yml b/modules/nf-core/chewbbaca/createschema/meta.yml index 6e2006a99cb..eed0daf29ea 100644 --- a/modules/nf-core/chewbbaca/createschema/meta.yml +++ b/modules/nf-core/chewbbaca/createschema/meta.yml @@ -1,6 +1,6 @@ --- name: "chewbbaca_createschema" -description: write your description here +description: Create a schema to determine the allelic profiles of a genome keywords: - cgMLST - WGS @@ -22,12 +22,12 @@ input: description: | Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]` - + - fasta: type: directory description: One or multiple FASTA files to create schema from pattern: "*.{fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz}" - + - prodigal_tf: type: file description: File containing the prodigal training file @@ -36,22 +36,28 @@ input: - cds: type: file description: File containing the prodigal cds file - pattern: "*.cds" - + pattern: "*.cds" ## TODO nf-core: Add a description of all of the variables used as output output: - - versions: type: file description: File containing software versions pattern: "versions.yml" - + - schema_dir: type: directory description: schema directory pattern: "*/" - + + - tsv: + type: file + description: file contains the coordinates of the CDS in the input sample + pattern: "*_cds_coordinates.tsv" + - txt: + type: file + description: file contains the list of alleles predicted by Prodigal that were excluded + pattern: "*_invalid_cds.txt" authors: - "@anwarMZ" diff --git a/tests/modules/nf-core/chewbbaca/createschema/main.nf b/tests/modules/nf-core/chewbbaca/createschema/main.nf index 33cf31aea04..7eb7dfbd8be 100644 --- a/tests/modules/nf-core/chewbbaca/createschema/main.nf +++ b/tests/modules/nf-core/chewbbaca/createschema/main.nf @@ -26,3 +26,15 @@ workflow test_chewbbaca_createschema_multi { CHEWBBACA_CREATESCHEMA ( input, ptf, cds) } + +workflow test_chewbbaca_createschema_gz { + + input = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true)] ] + ptf = [] + cds = [] + + CHEWBBACA_CREATESCHEMA ( input, ptf, cds) +} \ No newline at end of file diff --git a/tests/modules/nf-core/chewbbaca/createschema/test.yml b/tests/modules/nf-core/chewbbaca/createschema/test.yml index 88965bd7e23..6e08a1d073e 100644 --- a/tests/modules/nf-core/chewbbaca/createschema/test.yml +++ b/tests/modules/nf-core/chewbbaca/createschema/test.yml @@ -155,3 +155,80 @@ - path: output/chewbbaca/results/test/short/genome-protein1_short.fasta md5sum: c1b28842a7e89e3bcc7d655afe51c609 - path: output/chewbbaca/versions.yml + +- name: chewbbaca createschema test_chewbbaca_createschema_gz + command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema_gz -c ./tests/config/nextflow.config + tags: + - chewbbaca + - chewbbaca/createschema + files: + - path: output/chewbbaca/results/cds_coordinates.tsv + md5sum: e62f4e808939f97ccdbe4d17c1521b6c + - path: output/chewbbaca/results/invalid_cds.txt + md5sum: d0afbd9996054d8838e62dc3e852fa07 + - path: output/chewbbaca/results/test/.genes_list + contains: + - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ' + - path: output/chewbbaca/results/test/.schema_config + md5sum: 92b512f65fde7dce321ada54e5c431e9 + - path: output/chewbbaca/results/test/contigs-protein1.fasta + md5sum: 79f1e1c7105c0b34195e18c34960d2d4 + - path: output/chewbbaca/results/test/contigs-protein10.fasta + md5sum: 9fd40f7247cb3ed93f66828dbbfbac22 + - path: output/chewbbaca/results/test/contigs-protein14.fasta + md5sum: 2a8023e86fb119834f2d050daee33958 + - path: output/chewbbaca/results/test/contigs-protein16.fasta + md5sum: e006bb0da17f845c1672caed826d4ab7 + - path: output/chewbbaca/results/test/contigs-protein17.fasta + md5sum: 58f2501c0a7e48aaa86a87d01740b5c4 + - path: output/chewbbaca/results/test/contigs-protein18.fasta + md5sum: 6b4f385dc954df1fd2057a1c57872338 + - path: output/chewbbaca/results/test/contigs-protein19.fasta + md5sum: 3614c079d0b08f0c59bdaac9dcea0409 + - path: output/chewbbaca/results/test/contigs-protein2.fasta + md5sum: 0b982a66a0f001f11a86cc1b5a4ef80d + - path: output/chewbbaca/results/test/contigs-protein20.fasta + md5sum: 75b2492e5db0848079faafe6f60fe9fd + - path: output/chewbbaca/results/test/contigs-protein4.fasta + md5sum: 4ce5090bf2547bc588f0f8d00ae4a59d + - path: output/chewbbaca/results/test/contigs-protein6.fasta + md5sum: ffebf19b61285767a14f486af7181c30 + - path: output/chewbbaca/results/test/contigs-protein7.fasta + md5sum: ee06d9303c5b7844b003daa42b7a1869 + - path: output/chewbbaca/results/test/contigs-protein8.fasta + md5sum: 2a00efc36b036ab7f6c30f85533963cf + - path: output/chewbbaca/results/test/contigs-protein9.fasta + md5sum: ad9372b812030db327fa12d1e1731e85 + - path: output/chewbbaca/results/test/genome-protein1.fasta + md5sum: c1b28842a7e89e3bcc7d655afe51c609 + - path: output/chewbbaca/results/test/short/contigs-protein10_short.fasta + md5sum: 9fd40f7247cb3ed93f66828dbbfbac22 + - path: output/chewbbaca/results/test/short/contigs-protein14_short.fasta + md5sum: 2a8023e86fb119834f2d050daee33958 + - path: output/chewbbaca/results/test/short/contigs-protein16_short.fasta + md5sum: e006bb0da17f845c1672caed826d4ab7 + - path: output/chewbbaca/results/test/short/contigs-protein17_short.fasta + md5sum: 58f2501c0a7e48aaa86a87d01740b5c4 + - path: output/chewbbaca/results/test/short/contigs-protein18_short.fasta + md5sum: 6b4f385dc954df1fd2057a1c57872338 + - path: output/chewbbaca/results/test/short/contigs-protein19_short.fasta + md5sum: 3614c079d0b08f0c59bdaac9dcea0409 + - path: output/chewbbaca/results/test/short/contigs-protein1_short.fasta + md5sum: 79f1e1c7105c0b34195e18c34960d2d4 + - path: output/chewbbaca/results/test/short/contigs-protein20_short.fasta + md5sum: 75b2492e5db0848079faafe6f60fe9fd + - path: output/chewbbaca/results/test/short/contigs-protein2_short.fasta + md5sum: 0b982a66a0f001f11a86cc1b5a4ef80d + - path: output/chewbbaca/results/test/short/contigs-protein4_short.fasta + md5sum: 4ce5090bf2547bc588f0f8d00ae4a59d + - path: output/chewbbaca/results/test/short/contigs-protein6_short.fasta + md5sum: ffebf19b61285767a14f486af7181c30 + - path: output/chewbbaca/results/test/short/contigs-protein7_short.fasta + md5sum: ee06d9303c5b7844b003daa42b7a1869 + - path: output/chewbbaca/results/test/short/contigs-protein8_short.fasta + md5sum: 2a00efc36b036ab7f6c30f85533963cf + - path: output/chewbbaca/results/test/short/contigs-protein9_short.fasta + md5sum: ad9372b812030db327fa12d1e1731e85 + - path: output/chewbbaca/results/test/short/genome-protein1_short.fasta + md5sum: c1b28842a7e89e3bcc7d655afe51c609 + - path: output/chewbbaca/versions.yml From 519a57251d3d5c2390a4c7c0b40c6f87b967f5fa Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Wed, 29 Nov 2023 11:13:01 -0800 Subject: [PATCH 03/25] update the formatting --- tests/modules/nf-core/chewbbaca/createschema/test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/modules/nf-core/chewbbaca/createschema/test.yml b/tests/modules/nf-core/chewbbaca/createschema/test.yml index 6e08a1d073e..23a603c8fc8 100644 --- a/tests/modules/nf-core/chewbbaca/createschema/test.yml +++ b/tests/modules/nf-core/chewbbaca/createschema/test.yml @@ -10,7 +10,7 @@ md5sum: d0afbd9996054d8838e62dc3e852fa07 - path: output/chewbbaca/results/test/.genes_list contains: - - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ' + - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead " - path: output/chewbbaca/results/test/.schema_config md5sum: 92b512f65fde7dce321ada54e5c431e9 - path: output/chewbbaca/results/test/contigs-protein1.fasta @@ -91,7 +91,7 @@ md5sum: d0afbd9996054d8838e62dc3e852fa07 - path: output/chewbbaca/results/test/.genes_list contains: - - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ' + - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead " - path: output/chewbbaca/results/test/.schema_config md5sum: 92b512f65fde7dce321ada54e5c431e9 - path: output/chewbbaca/results/test/contigs-protein1.fasta @@ -168,7 +168,7 @@ md5sum: d0afbd9996054d8838e62dc3e852fa07 - path: output/chewbbaca/results/test/.genes_list contains: - - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ' + - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead " - path: output/chewbbaca/results/test/.schema_config md5sum: 92b512f65fde7dce321ada54e5c431e9 - path: output/chewbbaca/results/test/contigs-protein1.fasta From a2e9a157225e70d91efec90cce4c55052e838632 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Wed, 29 Nov 2023 11:46:25 -0800 Subject: [PATCH 04/25] update the formatting --- modules/nf-core/chewbbaca/createschema/main.nf | 6 +----- .../modules/nf-core/chewbbaca/createschema/main.nf | 14 +++++++------- 2 files changed, 8 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf index 29f97d0dc71..cac8ae3bf88 100644 --- a/modules/nf-core/chewbbaca/createschema/main.nf +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -11,8 +11,7 @@ process CHEWBBACA_CREATESCHEMA { tuple val(meta), path(fasta, stageAs: "input_genomes/*") path prodigal_tf path cds - - + output: path 'results/*' , emit: schema path "results/cds_coordinates.tsv" , emit: cds_coordinates @@ -41,7 +40,6 @@ process CHEWBBACA_CREATESCHEMA { $prodigal_tf \\ $cds \\ --cpu $task.cpus - cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -53,12 +51,10 @@ process CHEWBBACA_CREATESCHEMA { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def schema = "--n ${prefix}" - """ mkdir -p results/$schema - cat <<-END_VERSIONS > versions.yml "${task.process}": chewbbaca: \$(echo \$(chewie --version 2>&1 | sed 's/^.*chewBBACA version: //g; s/Using.*\$//' )) diff --git a/tests/modules/nf-core/chewbbaca/createschema/main.nf b/tests/modules/nf-core/chewbbaca/createschema/main.nf index 7eb7dfbd8be..c21fe3c37d8 100644 --- a/tests/modules/nf-core/chewbbaca/createschema/main.nf +++ b/tests/modules/nf-core/chewbbaca/createschema/main.nf @@ -5,36 +5,36 @@ nextflow.enable.dsl = 2 include { CHEWBBACA_CREATESCHEMA } from '../../../../../modules/nf-core/chewbbaca/createschema/main.nf' workflow test_chewbbaca_createschema { - + input = [ [ id:'test', single_end:false ], // meta map file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)] ptf = [] cds = [] - + CHEWBBACA_CREATESCHEMA ( input, ptf, cds) } workflow test_chewbbaca_createschema_multi { - + input = [ [ id:'test', single_end:false ], // meta map [ file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] ] ptf = [] cds = [] - + CHEWBBACA_CREATESCHEMA ( input, ptf, cds) } workflow test_chewbbaca_createschema_gz { - + input = [ [ id:'test', single_end:false ], // meta map [ file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true)] ] ptf = [] cds = [] - + CHEWBBACA_CREATESCHEMA ( input, ptf, cds) -} \ No newline at end of file +} From f507c31d975ead7317bd9f9b1d52b941bfadbb07 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Tue, 5 Dec 2023 22:53:41 -0800 Subject: [PATCH 05/25] updated module to emit meta --- modules/nf-core/chewbbaca/createschema/main.nf | 2 +- .../nf-core/chewbbaca/createschema/meta.yml | 9 +++++++-- .../nf-core/chewbbaca/createschema/test.yml | 18 +++++++++--------- 3 files changed, 17 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf index cac8ae3bf88..b009884c96f 100644 --- a/modules/nf-core/chewbbaca/createschema/main.nf +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -13,7 +13,7 @@ process CHEWBBACA_CREATESCHEMA { path cds output: - path 'results/*' , emit: schema + tuple val(meta), path("results/$meta.id") , emit: schema path "results/cds_coordinates.tsv" , emit: cds_coordinates path "results/invalid_cds.txt" , emit: invalid_cds path "versions.yml" , emit: versions diff --git a/modules/nf-core/chewbbaca/createschema/meta.yml b/modules/nf-core/chewbbaca/createschema/meta.yml index eed0daf29ea..71cc51ef5e2 100644 --- a/modules/nf-core/chewbbaca/createschema/meta.yml +++ b/modules/nf-core/chewbbaca/createschema/meta.yml @@ -14,7 +14,6 @@ tools: doi: "10.1099/mgen.0.000166" licence: ["GPL v3"] -## TODO nf-core: Add a description of all of the variables used as input input: # Only when we have meta - meta: @@ -38,13 +37,18 @@ input: description: File containing the prodigal cds file pattern: "*.cds" -## TODO nf-core: Add a description of all of the variables used as output output: - versions: type: file description: File containing software versions pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - schema_dir: type: directory description: schema directory @@ -54,6 +58,7 @@ output: type: file description: file contains the coordinates of the CDS in the input sample pattern: "*_cds_coordinates.tsv" + - txt: type: file description: file contains the list of alleles predicted by Prodigal that were excluded diff --git a/tests/modules/nf-core/chewbbaca/createschema/test.yml b/tests/modules/nf-core/chewbbaca/createschema/test.yml index 23a603c8fc8..54a737c5a92 100644 --- a/tests/modules/nf-core/chewbbaca/createschema/test.yml +++ b/tests/modules/nf-core/chewbbaca/createschema/test.yml @@ -1,8 +1,8 @@ - name: chewbbaca createschema test_chewbbaca_createschema - command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema -c ./tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chewbbaca/createschema/nextflow.config tags: - - chewbbaca - chewbbaca/createschema + - chewbbaca files: - path: output/chewbbaca/results/cds_coordinates.tsv md5sum: 7fef49207aa024b68f465e986f4c7444 @@ -10,7 +10,7 @@ md5sum: d0afbd9996054d8838e62dc3e852fa07 - path: output/chewbbaca/results/test/.genes_list contains: - - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead " + - '00000000' - path: output/chewbbaca/results/test/.schema_config md5sum: 92b512f65fde7dce321ada54e5c431e9 - path: output/chewbbaca/results/test/contigs-protein1.fasta @@ -80,10 +80,10 @@ - path: output/chewbbaca/versions.yml - name: chewbbaca createschema test_chewbbaca_createschema_multi - command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema_multi -c ./tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema_multi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chewbbaca/createschema/nextflow.config tags: - - chewbbaca - chewbbaca/createschema + - chewbbaca files: - path: output/chewbbaca/results/cds_coordinates.tsv md5sum: e62f4e808939f97ccdbe4d17c1521b6c @@ -91,7 +91,7 @@ md5sum: d0afbd9996054d8838e62dc3e852fa07 - path: output/chewbbaca/results/test/.genes_list contains: - - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead " + - '00000000' - path: output/chewbbaca/results/test/.schema_config md5sum: 92b512f65fde7dce321ada54e5c431e9 - path: output/chewbbaca/results/test/contigs-protein1.fasta @@ -157,10 +157,10 @@ - path: output/chewbbaca/versions.yml - name: chewbbaca createschema test_chewbbaca_createschema_gz - command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema_gz -c ./tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema_gz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chewbbaca/createschema/nextflow.config tags: - - chewbbaca - chewbbaca/createschema + - chewbbaca files: - path: output/chewbbaca/results/cds_coordinates.tsv md5sum: e62f4e808939f97ccdbe4d17c1521b6c @@ -168,7 +168,7 @@ md5sum: d0afbd9996054d8838e62dc3e852fa07 - path: output/chewbbaca/results/test/.genes_list contains: - - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead " + - '00000000' - path: output/chewbbaca/results/test/.schema_config md5sum: 92b512f65fde7dce321ada54e5c431e9 - path: output/chewbbaca/results/test/contigs-protein1.fasta From 1570c80d2522c51d002bfeee0242391401754b3d Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Tue, 5 Dec 2023 23:28:10 -0800 Subject: [PATCH 06/25] updated test.yml --- .../nf-core/chewbbaca/createschema/test.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/tests/modules/nf-core/chewbbaca/createschema/test.yml b/tests/modules/nf-core/chewbbaca/createschema/test.yml index 54a737c5a92..36392d29322 100644 --- a/tests/modules/nf-core/chewbbaca/createschema/test.yml +++ b/tests/modules/nf-core/chewbbaca/createschema/test.yml @@ -1,8 +1,8 @@ - name: chewbbaca createschema test_chewbbaca_createschema - command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chewbbaca/createschema/nextflow.config + command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema -c ./tests/config/nextflow.config tags: - - chewbbaca/createschema - chewbbaca + - chewbbaca/createschema files: - path: output/chewbbaca/results/cds_coordinates.tsv md5sum: 7fef49207aa024b68f465e986f4c7444 @@ -10,7 +10,7 @@ md5sum: d0afbd9996054d8838e62dc3e852fa07 - path: output/chewbbaca/results/test/.genes_list contains: - - '00000000' + - "contigs-" - path: output/chewbbaca/results/test/.schema_config md5sum: 92b512f65fde7dce321ada54e5c431e9 - path: output/chewbbaca/results/test/contigs-protein1.fasta @@ -80,10 +80,10 @@ - path: output/chewbbaca/versions.yml - name: chewbbaca createschema test_chewbbaca_createschema_multi - command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema_multi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chewbbaca/createschema/nextflow.config + command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema_multi -c ./tests/config/nextflow.config tags: - - chewbbaca/createschema - chewbbaca + - chewbbaca/createschema files: - path: output/chewbbaca/results/cds_coordinates.tsv md5sum: e62f4e808939f97ccdbe4d17c1521b6c @@ -91,7 +91,7 @@ md5sum: d0afbd9996054d8838e62dc3e852fa07 - path: output/chewbbaca/results/test/.genes_list contains: - - '00000000' + - "contigs-" - path: output/chewbbaca/results/test/.schema_config md5sum: 92b512f65fde7dce321ada54e5c431e9 - path: output/chewbbaca/results/test/contigs-protein1.fasta @@ -157,10 +157,10 @@ - path: output/chewbbaca/versions.yml - name: chewbbaca createschema test_chewbbaca_createschema_gz - command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema_gz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chewbbaca/createschema/nextflow.config + command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema_gz -c ./tests/config/nextflow.config tags: - - chewbbaca/createschema - chewbbaca + - chewbbaca/createschema files: - path: output/chewbbaca/results/cds_coordinates.tsv md5sum: e62f4e808939f97ccdbe4d17c1521b6c @@ -168,7 +168,7 @@ md5sum: d0afbd9996054d8838e62dc3e852fa07 - path: output/chewbbaca/results/test/.genes_list contains: - - '00000000' + - "contigs-" - path: output/chewbbaca/results/test/.schema_config md5sum: 92b512f65fde7dce321ada54e5c431e9 - path: output/chewbbaca/results/test/contigs-protein1.fasta From 6113a217857475786db1ca86cef6f9415096d809 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Wed, 6 Dec 2023 10:20:03 -0800 Subject: [PATCH 07/25] update pytest --- tests/modules/nf-core/chewbbaca/createschema/test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/modules/nf-core/chewbbaca/createschema/test.yml b/tests/modules/nf-core/chewbbaca/createschema/test.yml index 36392d29322..6e08a1d073e 100644 --- a/tests/modules/nf-core/chewbbaca/createschema/test.yml +++ b/tests/modules/nf-core/chewbbaca/createschema/test.yml @@ -10,7 +10,7 @@ md5sum: d0afbd9996054d8838e62dc3e852fa07 - path: output/chewbbaca/results/test/.genes_list contains: - - "contigs-" + - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ' - path: output/chewbbaca/results/test/.schema_config md5sum: 92b512f65fde7dce321ada54e5c431e9 - path: output/chewbbaca/results/test/contigs-protein1.fasta @@ -91,7 +91,7 @@ md5sum: d0afbd9996054d8838e62dc3e852fa07 - path: output/chewbbaca/results/test/.genes_list contains: - - "contigs-" + - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ' - path: output/chewbbaca/results/test/.schema_config md5sum: 92b512f65fde7dce321ada54e5c431e9 - path: output/chewbbaca/results/test/contigs-protein1.fasta @@ -168,7 +168,7 @@ md5sum: d0afbd9996054d8838e62dc3e852fa07 - path: output/chewbbaca/results/test/.genes_list contains: - - "contigs-" + - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ' - path: output/chewbbaca/results/test/.schema_config md5sum: 92b512f65fde7dce321ada54e5c431e9 - path: output/chewbbaca/results/test/contigs-protein1.fasta From 313b1e44b1150e312dd53240481c7cff9b425dda Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Fri, 5 Jan 2024 11:34:50 -0800 Subject: [PATCH 08/25] clean the meta.yml --- modules/nf-core/chewbbaca/createschema/meta.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/nf-core/chewbbaca/createschema/meta.yml b/modules/nf-core/chewbbaca/createschema/meta.yml index 71cc51ef5e2..cdcd1e0e2a9 100644 --- a/modules/nf-core/chewbbaca/createschema/meta.yml +++ b/modules/nf-core/chewbbaca/createschema/meta.yml @@ -15,7 +15,6 @@ tools: licence: ["GPL v3"] input: - # Only when we have meta - meta: type: map description: | From e9f4aad1eb86d99005c33516c4223c923d6301da Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Fri, 5 Jan 2024 11:36:12 -0800 Subject: [PATCH 09/25] clean the meta.yml --- modules/nf-core/chewbbaca/createschema/meta.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/nf-core/chewbbaca/createschema/meta.yml b/modules/nf-core/chewbbaca/createschema/meta.yml index cdcd1e0e2a9..65170c90c87 100644 --- a/modules/nf-core/chewbbaca/createschema/meta.yml +++ b/modules/nf-core/chewbbaca/createschema/meta.yml @@ -1,4 +1,3 @@ ---- name: "chewbbaca_createschema" description: Create a schema to determine the allelic profiles of a genome keywords: From 90fb055433db67c5405517e26b5a60e9092f7a5e Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Fri, 5 Jan 2024 11:37:38 -0800 Subject: [PATCH 10/25] clean the meta.yml --- modules/nf-core/chewbbaca/createschema/meta.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/meta.yml b/modules/nf-core/chewbbaca/createschema/meta.yml index 65170c90c87..0b3a4c369cc 100644 --- a/modules/nf-core/chewbbaca/createschema/meta.yml +++ b/modules/nf-core/chewbbaca/createschema/meta.yml @@ -1,11 +1,11 @@ -name: "chewbbaca_createschema" +name: chewbbaca_createschema description: Create a schema to determine the allelic profiles of a genome keywords: - cgMLST - WGS - genomics tools: - - "chewbbaca": + - chewbbaca: description: "A complete suite for gene-by-gene schema creation and strain identification." homepage: "https://chewbbaca.readthedocs.io/en/latest/index.html" documentation: "https://chewbbaca.readthedocs.io/en/latest/index.html" From ecbaa6347c8ec4c6e64d6ae8a861371ae75276f1 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Fri, 5 Jan 2024 12:02:25 -0800 Subject: [PATCH 11/25] replaced conda package with environment.yml file --- modules/nf-core/chewbbaca/createschema/environment.yml | 7 +++++++ modules/nf-core/chewbbaca/createschema/main.nf | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) create mode 100644 modules/nf-core/chewbbaca/createschema/environment.yml diff --git a/modules/nf-core/chewbbaca/createschema/environment.yml b/modules/nf-core/chewbbaca/createschema/environment.yml new file mode 100644 index 00000000000..9788ebbccfa --- /dev/null +++ b/modules/nf-core/chewbbaca/createschema/environment.yml @@ -0,0 +1,7 @@ +name: chewbbaca_createschema +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::chewbbaca=3.3.1 diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf index b009884c96f..4b9875869a2 100644 --- a/modules/nf-core/chewbbaca/createschema/main.nf +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -2,7 +2,7 @@ process CHEWBBACA_CREATESCHEMA { tag "$meta.id" label 'process_low' - conda "bioconda::chewbbaca=3.3.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/chewbbaca:3.3.1--pyhdfd78af_0': 'biocontainers/chewbbaca:3.3.1--pyhdfd78af_0' }" From 09adb4179f3cca5d53e586c0e4bc57ae1c92c5c1 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Fri, 5 Jan 2024 14:03:33 -0800 Subject: [PATCH 12/25] py-test to nf-test migration --- .../chewbbaca/createschema/tests/main.nf.test | 91 ++ .../createschema/tests/main.nf.test.snap | 236 +++++ .../createschema/tests}/nextflow.config | 4 +- .../chewbbaca/createschema/tests/tags.yml | 2 + tests/config/pytest_modules.yml | 955 ------------------ .../nf-core/chewbbaca/createschema/main.nf | 40 - .../nf-core/chewbbaca/createschema/test.yml | 234 ----- 7 files changed, 330 insertions(+), 1232 deletions(-) create mode 100644 modules/nf-core/chewbbaca/createschema/tests/main.nf.test create mode 100644 modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap rename {tests/modules/nf-core/chewbbaca/createschema => modules/nf-core/chewbbaca/createschema/tests}/nextflow.config (94%) create mode 100644 modules/nf-core/chewbbaca/createschema/tests/tags.yml delete mode 100644 tests/modules/nf-core/chewbbaca/createschema/main.nf delete mode 100644 tests/modules/nf-core/chewbbaca/createschema/test.yml diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test new file mode 100644 index 00000000000..e4ff159c51f --- /dev/null +++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test @@ -0,0 +1,91 @@ +nextflow_process { + + name "Test Process CHEWBBACA_CREATESCHEMA" + script "../main.nf" + process "CHEWBBACA_CREATESCHEMA" + + tag "modules" + tag "modules_nfcore" + tag "chewbbaca" + tag "chewbbaca/createschema" + + test("test_chewbbaca_createschema_single") { + + when { + process { + + """ + + ptf = [] + cds = [] + input[0] = [[ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)] + input[1] = ptf + input[2] = cds + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_chewbbaca_createschema_multi") { + + when { + process { + + """ + + ptf = [] + cds = [] + input[0] = = [[ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[1] = ptf + input[2] = cds + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_chewbbaca_createschema_gz") { + + when { + process { + + """ + + ptf = [] + cds = [] + input[0] = [[ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true)] + input[1] = ptf + input[2] = cds + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } +} diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap new file mode 100644 index 00000000000..3f081e1d4ef --- /dev/null +++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap @@ -0,0 +1,236 @@ +{ + "test_chewbbaca_createschema_gz": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + ".genes_list:md5,2ffc5e37f87962d27169cfc3e20d1f96", + ".schema_config:md5,92b512f65fde7dce321ada54e5c431e9", + "contigs-protein1.fasta:md5,79f1e1c7105c0b34195e18c34960d2d4", + "contigs-protein10.fasta:md5,9fd40f7247cb3ed93f66828dbbfbac22", + "contigs-protein11.fasta:md5,b2f94d1babce56f5c1e46ccd35d2a7d7", + "contigs-protein13.fasta:md5,7314303d55a8598b229eca32ddeea14d", + "contigs-protein14.fasta:md5,2a8023e86fb119834f2d050daee33958", + "contigs-protein16.fasta:md5,e006bb0da17f845c1672caed826d4ab7", + "contigs-protein17.fasta:md5,58f2501c0a7e48aaa86a87d01740b5c4", + "contigs-protein18.fasta:md5,6b4f385dc954df1fd2057a1c57872338", + "contigs-protein19.fasta:md5,3614c079d0b08f0c59bdaac9dcea0409", + "contigs-protein2.fasta:md5,0b982a66a0f001f11a86cc1b5a4ef80d", + "contigs-protein20.fasta:md5,75b2492e5db0848079faafe6f60fe9fd", + "contigs-protein4.fasta:md5,4ce5090bf2547bc588f0f8d00ae4a59d", + "contigs-protein6.fasta:md5,ffebf19b61285767a14f486af7181c30", + "contigs-protein7.fasta:md5,ee06d9303c5b7844b003daa42b7a1869", + "contigs-protein8.fasta:md5,2a00efc36b036ab7f6c30f85533963cf", + "contigs-protein9.fasta:md5,ad9372b812030db327fa12d1e1731e85", + [ + "contigs-protein10_short.fasta:md5,9fd40f7247cb3ed93f66828dbbfbac22", + "contigs-protein11_short.fasta:md5,b2f94d1babce56f5c1e46ccd35d2a7d7", + 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"contigs-protein4.fasta:md5,4ce5090bf2547bc588f0f8d00ae4a59d", + "contigs-protein6.fasta:md5,ffebf19b61285767a14f486af7181c30", + "contigs-protein7.fasta:md5,ee06d9303c5b7844b003daa42b7a1869", + "contigs-protein8.fasta:md5,2a00efc36b036ab7f6c30f85533963cf", + "contigs-protein9.fasta:md5,ad9372b812030db327fa12d1e1731e85", + [ + "contigs-protein10_short.fasta:md5,9fd40f7247cb3ed93f66828dbbfbac22", + "contigs-protein11_short.fasta:md5,b2f94d1babce56f5c1e46ccd35d2a7d7", + "contigs-protein13_short.fasta:md5,7314303d55a8598b229eca32ddeea14d", + "contigs-protein14_short.fasta:md5,2a8023e86fb119834f2d050daee33958", + "contigs-protein16_short.fasta:md5,e006bb0da17f845c1672caed826d4ab7", + "contigs-protein17_short.fasta:md5,58f2501c0a7e48aaa86a87d01740b5c4", + "contigs-protein18_short.fasta:md5,6b4f385dc954df1fd2057a1c57872338", + "contigs-protein19_short.fasta:md5,3614c079d0b08f0c59bdaac9dcea0409", + "contigs-protein1_short.fasta:md5,79f1e1c7105c0b34195e18c34960d2d4", + "contigs-protein20_short.fasta:md5,75b2492e5db0848079faafe6f60fe9fd", + "contigs-protein2_short.fasta:md5,0b982a66a0f001f11a86cc1b5a4ef80d", + "contigs-protein4_short.fasta:md5,4ce5090bf2547bc588f0f8d00ae4a59d", + "contigs-protein6_short.fasta:md5,ffebf19b61285767a14f486af7181c30", + "contigs-protein7_short.fasta:md5,ee06d9303c5b7844b003daa42b7a1869", + "contigs-protein8_short.fasta:md5,2a00efc36b036ab7f6c30f85533963cf", + "contigs-protein9_short.fasta:md5,ad9372b812030db327fa12d1e1731e85" + ] + ] + ] + ], + "1": [ + "cds_coordinates.tsv:md5,7fef49207aa024b68f465e986f4c7444" + ], + "2": [ + "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" + ], + "3": [ + "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" + ], + "cds_coordinates": [ + "cds_coordinates.tsv:md5,7fef49207aa024b68f465e986f4c7444" + ], + "invalid_cds": [ + "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" + ], + "schema": [ + [ + { + "id": "test", + "single_end": false + }, + [ + ".genes_list:md5,976cb1267b9b994237c0c5e58fdeae9d", + ".schema_config:md5,92b512f65fde7dce321ada54e5c431e9", + "contigs-protein1.fasta:md5,79f1e1c7105c0b34195e18c34960d2d4", + "contigs-protein10.fasta:md5,9fd40f7247cb3ed93f66828dbbfbac22", + "contigs-protein11.fasta:md5,b2f94d1babce56f5c1e46ccd35d2a7d7", + "contigs-protein13.fasta:md5,7314303d55a8598b229eca32ddeea14d", + "contigs-protein14.fasta:md5,2a8023e86fb119834f2d050daee33958", + "contigs-protein16.fasta:md5,e006bb0da17f845c1672caed826d4ab7", + "contigs-protein17.fasta:md5,58f2501c0a7e48aaa86a87d01740b5c4", + "contigs-protein18.fasta:md5,6b4f385dc954df1fd2057a1c57872338", + "contigs-protein19.fasta:md5,3614c079d0b08f0c59bdaac9dcea0409", + "contigs-protein2.fasta:md5,0b982a66a0f001f11a86cc1b5a4ef80d", + "contigs-protein20.fasta:md5,75b2492e5db0848079faafe6f60fe9fd", + "contigs-protein4.fasta:md5,4ce5090bf2547bc588f0f8d00ae4a59d", + "contigs-protein6.fasta:md5,ffebf19b61285767a14f486af7181c30", + "contigs-protein7.fasta:md5,ee06d9303c5b7844b003daa42b7a1869", + "contigs-protein8.fasta:md5,2a00efc36b036ab7f6c30f85533963cf", + "contigs-protein9.fasta:md5,ad9372b812030db327fa12d1e1731e85", + [ + "contigs-protein10_short.fasta:md5,9fd40f7247cb3ed93f66828dbbfbac22", + "contigs-protein11_short.fasta:md5,b2f94d1babce56f5c1e46ccd35d2a7d7", + "contigs-protein13_short.fasta:md5,7314303d55a8598b229eca32ddeea14d", + "contigs-protein14_short.fasta:md5,2a8023e86fb119834f2d050daee33958", + "contigs-protein16_short.fasta:md5,e006bb0da17f845c1672caed826d4ab7", + "contigs-protein17_short.fasta:md5,58f2501c0a7e48aaa86a87d01740b5c4", + "contigs-protein18_short.fasta:md5,6b4f385dc954df1fd2057a1c57872338", + "contigs-protein19_short.fasta:md5,3614c079d0b08f0c59bdaac9dcea0409", + "contigs-protein1_short.fasta:md5,79f1e1c7105c0b34195e18c34960d2d4", + "contigs-protein20_short.fasta:md5,75b2492e5db0848079faafe6f60fe9fd", + "contigs-protein2_short.fasta:md5,0b982a66a0f001f11a86cc1b5a4ef80d", + "contigs-protein4_short.fasta:md5,4ce5090bf2547bc588f0f8d00ae4a59d", + "contigs-protein6_short.fasta:md5,ffebf19b61285767a14f486af7181c30", + "contigs-protein7_short.fasta:md5,ee06d9303c5b7844b003daa42b7a1869", + "contigs-protein8_short.fasta:md5,2a00efc36b036ab7f6c30f85533963cf", + "contigs-protein9_short.fasta:md5,ad9372b812030db327fa12d1e1731e85" + ] + ] + ] + ], + "versions": [ + "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" + ] + } + ], + "timestamp": "2024-01-05T13:37:51.898568" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/chewbbaca/createschema/nextflow.config b/modules/nf-core/chewbbaca/createschema/tests/nextflow.config similarity index 94% rename from tests/modules/nf-core/chewbbaca/createschema/nextflow.config rename to modules/nf-core/chewbbaca/createschema/tests/nextflow.config index 50f50a7a357..0293c16f9ee 100644 --- a/tests/modules/nf-core/chewbbaca/createschema/nextflow.config +++ b/modules/nf-core/chewbbaca/createschema/tests/nextflow.config @@ -1,5 +1,3 @@ process { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file +} diff --git a/modules/nf-core/chewbbaca/createschema/tests/tags.yml b/modules/nf-core/chewbbaca/createschema/tests/tags.yml new file mode 100644 index 00000000000..c611ab64aeb --- /dev/null +++ b/modules/nf-core/chewbbaca/createschema/tests/tags.yml @@ -0,0 +1,2 @@ +chewbbaca/createschema: + - "modules/nf-core/chewbbaca/createschema/**" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index b42c18e61b1..12908e7eae2 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1,504 +1,381 @@ abritamr/run: - modules/nf-core/abritamr/run/** - tests/modules/nf-core/abritamr/run/** - adapterremoval: - modules/nf-core/adapterremoval/** - tests/modules/nf-core/adapterremoval/** - adapterremovalfixprefix: - modules/nf-core/adapterremovalfixprefix/** - tests/modules/nf-core/adapterremovalfixprefix/** - admixture: - modules/nf-core/admixture/** - tests/modules/nf-core/admixture/** - affy/justrma: - modules/nf-core/affy/justrma/** - tests/modules/nf-core/affy/justrma/** - agat/convertspgff2gtf: - modules/nf-core/agat/convertspgff2gtf/** - tests/modules/nf-core/agat/convertspgff2gtf/** - agat/convertspgff2tsv: - modules/nf-core/agat/convertspgff2tsv/** - tests/modules/nf-core/agat/convertspgff2tsv/** - agat/convertspgxf2gxf: - modules/nf-core/agat/convertspgxf2gxf/** - tests/modules/nf-core/agat/convertspgxf2gxf/** - agat/spstatistics: - modules/nf-core/agat/spstatistics/** - tests/modules/nf-core/agat/spstatistics/** - agat/sqstatbasic: - modules/nf-core/agat/sqstatbasic/** - tests/modules/nf-core/agat/sqstatbasic/** - agrvate: - modules/nf-core/agrvate/** - tests/modules/nf-core/agrvate/** - allelecounter: - modules/nf-core/allelecounter/** - tests/modules/nf-core/allelecounter/** - ampcombi: - modules/nf-core/ampcombi/** - tests/modules/nf-core/ampcombi/** - ampir: - modules/nf-core/ampir/** - tests/modules/nf-core/ampir/** - amps: - modules/nf-core/amps/** - tests/modules/nf-core/amps/** - amrfinderplus/run: - modules/nf-core/amrfinderplus/run/** - tests/modules/nf-core/amrfinderplus/run/** - amrfinderplus/update: - modules/nf-core/amrfinderplus/update/** - tests/modules/nf-core/amrfinderplus/update/** - angsd/contamination: - modules/nf-core/angsd/contamination/** - tests/modules/nf-core/angsd/contamination/** - angsd/docounts: - modules/nf-core/angsd/docounts/** - tests/modules/nf-core/angsd/docounts/** - annotsv/annotsv: - modules/nf-core/annotsv/annotsv/** - tests/modules/nf-core/annotsv/annotsv/** - annotsv/installannotations: - modules/nf-core/annotsv/installannotations/** - tests/modules/nf-core/annotsv/installannotations/** - antismash/antismashlite: - modules/nf-core/antismash/antismashlite/** - tests/modules/nf-core/antismash/antismashlite/** - antismash/antismashlitedownloaddatabases: - modules/nf-core/antismash/antismashlitedownloaddatabases/** - tests/modules/nf-core/antismash/antismashlitedownloaddatabases/** - arcashla/extract: - modules/nf-core/arcashla/extract/** - tests/modules/nf-core/arcashla/extract/** - ariba/getref: - modules/nf-core/ariba/getref/** - tests/modules/nf-core/ariba/getref/** - ariba/run: - modules/nf-core/ariba/run/** - tests/modules/nf-core/ariba/run/** - arriba/arriba: - modules/nf-core/arriba/arriba/** - tests/modules/nf-core/arriba/arriba/** - arriba/download: - modules/nf-core/arriba/download/** - tests/modules/nf-core/arriba/download/** - artic/guppyplex: - modules/nf-core/artic/guppyplex/** - tests/modules/nf-core/artic/guppyplex/** - artic/minion: - modules/nf-core/artic/minion/** - tests/modules/nf-core/artic/minion/** - ascat: - modules/nf-core/ascat/** - tests/modules/nf-core/ascat/** - ashlar: - modules/nf-core/ashlar/** - tests/modules/nf-core/ashlar/** - ataqv/ataqv: - modules/nf-core/ataqv/ataqv/** - tests/modules/nf-core/ataqv/ataqv/** - ataqv/mkarv: - modules/nf-core/ataqv/mkarv/** - tests/modules/nf-core/ataqv/mkarv/** - atlas/call: - modules/nf-core/atlas/call/** - tests/modules/nf-core/atlas/call/** - atlas/pmd: - modules/nf-core/atlas/pmd/** - tests/modules/nf-core/atlas/pmd/** - atlas/recal: - modules/nf-core/atlas/recal/** - tests/modules/nf-core/atlas/recal/** - atlas/splitmerge: - modules/nf-core/atlas/splitmerge/** - tests/modules/nf-core/atlas/splitmerge/** - atlasgeneannotationmanipulation/gtf2featureannotation: - modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/** - tests/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/** - authentict/deam2cont: - modules/nf-core/authentict/deam2cont/** - tests/modules/nf-core/authentict/deam2cont/** - bacphlip: - modules/nf-core/bacphlip/** - tests/modules/nf-core/bacphlip/** - bakta/bakta: - modules/nf-core/bakta/bakta/** - tests/modules/nf-core/bakta/bakta/** - bakta/baktadbdownload: - modules/nf-core/bakta/baktadbdownload/** - tests/modules/nf-core/bakta/baktadbdownload/** - bam2fastx/bam2fastq: - modules/nf-core/bam2fastx/bam2fastq/** - tests/modules/nf-core/bam2fastx/bam2fastq/** - bamaligncleaner: - modules/nf-core/bamaligncleaner/** - tests/modules/nf-core/bamaligncleaner/** - bamcmp: - modules/nf-core/bamcmp/** - tests/modules/nf-core/bamcmp/** - bamtools/convert: - modules/nf-core/bamtools/convert/** - tests/modules/nf-core/bamtools/convert/** - bamtools/split: - modules/nf-core/bamtools/split/** - tests/modules/nf-core/bamtools/split/** - bamtools/stats: - modules/nf-core/bamtools/stats/** - tests/modules/nf-core/bamtools/stats/** - bamutil/trimbam: - modules/nf-core/bamutil/trimbam/** - tests/modules/nf-core/bamutil/trimbam/** - bandage/image: - modules/nf-core/bandage/image/** - tests/modules/nf-core/bandage/image/** - barrnap: - modules/nf-core/barrnap/** - tests/modules/nf-core/barrnap/** - bases2fastq: - modules/nf-core/untar/** - modules/nf-core/bases2fastq/** - tests/modules/nf-core/bases2fastq/** - basicpy: - modules/nf-core/basicpy/** - tests/modules/nf-core/basicpy/** - bbmap/align: - modules/nf-core/bbmap/align/** - tests/modules/nf-core/bbmap/align/** - bbmap/bbduk: - modules/nf-core/bbmap/bbduk/** - tests/modules/nf-core/bbmap/bbduk/** - bbmap/bbnorm: - modules/nf-core/bbmap/bbnorm/** - tests/modules/nf-core/bbmap/bbnorm/** - bbmap/bbsplit: - modules/nf-core/bbmap/bbsplit/** - tests/modules/nf-core/bbmap/bbsplit/** - bbmap/clumpify: - modules/nf-core/bbmap/clumpify/** - tests/modules/nf-core/bbmap/clumpify/** - bbmap/index: - modules/nf-core/bbmap/index/** - tests/modules/nf-core/bbmap/index/** - bbmap/pileup: - modules/nf-core/bbmap/pileup/** - tests/modules/nf-core/bbmap/pileup/** - bbmap/sendsketch: - modules/nf-core/bbmap/sendsketch/** - tests/modules/nf-core/bbmap/sendsketch/** - bcftools/annotate: - modules/nf-core/bcftools/annotate/** - tests/modules/nf-core/bcftools/annotate/** - bcftools/consensus: - modules/nf-core/bcftools/consensus/** - tests/modules/nf-core/bcftools/consensus/** - bcftools/convert: - modules/nf-core/bcftools/convert/** - tests/modules/nf-core/bcftools/convert/** - bcftools/filter: - modules/nf-core/bcftools/filter/** - tests/modules/nf-core/bcftools/filter/** - bcftools/index: - modules/nf-core/bcftools/index/** - tests/modules/nf-core/bcftools/index** - bcftools/merge: - modules/nf-core/bcftools/merge/** - tests/modules/nf-core/bcftools/merge/** - bcftools/norm: - modules/nf-core/bcftools/norm/** - tests/modules/nf-core/bcftools/norm/** - bcftools/pluginscatter: - modules/nf-core/bcftools/pluginscatter/** - tests/modules/nf-core/bcftools/pluginscatter/** - bcftools/pluginsplit: - modules/nf-core/bcftools/pluginsplit/** - tests/modules/nf-core/bcftools/pluginsplit/** - bcftools/roh: - modules/nf-core/bcftools/roh/** - tests/modules/nf-core/bcftools/roh/** - bcftools/sort: - modules/nf-core/bcftools/sort/** - tests/modules/nf-core/bcftools/sort/** - bcftools/split: - modules/nf-core/bcftools/split/** - tests/modules/nf-core/bcftools/split/** - bcftools/stats: - modules/nf-core/bcftools/stats/** - tests/modules/nf-core/bcftools/stats/** - beagle5/beagle: - modules/nf-core/beagle5/beagle/** - tests/modules/nf-core/beagle5/beagle/** - bedtools/bamtobed: - modules/nf-core/bedtools/bamtobed/** - tests/modules/nf-core/bedtools/bamtobed/** - bedtools/closest: - modules/nf-core/bedtools/closest/** - tests/modules/nf-core/bedtools/closest/** - bedtools/complement: - modules/nf-core/bedtools/complement/** - tests/modules/nf-core/bedtools/complement/** - bedtools/coverage: - modules/nf-core/bedtools/coverage/** - tests/modules/nf-core/bedtools/coverage/** - bedtools/genomecov: - modules/nf-core/bedtools/genomecov/** - tests/modules/nf-core/bedtools/genomecov/** - bedtools/getfasta: - modules/nf-core/bedtools/getfasta/** - tests/modules/nf-core/bedtools/getfasta/** - bedtools/groupby: - modules/nf-core/bedtools/groupby/** - tests/modules/nf-core/bedtools/groupby/** - bedtools/intersect: - modules/nf-core/bedtools/intersect/** - tests/modules/nf-core/bedtools/intersect/** - bedtools/jaccard: - modules/nf-core/bedtools/jaccard/** - tests/modules/nf-core/bedtools/jaccard/** - bedtools/makewindows: - modules/nf-core/bedtools/makewindows/** - tests/modules/nf-core/bedtools/makewindows/** - bedtools/maskfasta: - modules/nf-core/bedtools/maskfasta/** - tests/modules/nf-core/bedtools/maskfasta/** - bedtools/merge: - modules/nf-core/bedtools/merge/** - tests/modules/nf-core/bedtools/merge/** - bedtools/multiinter: - modules/nf-core/bedtools/multiinter/** - tests/modules/nf-core/bedtools/multiinter/** - bedtools/shift: - modules/nf-core/bedtools/shift/** - tests/modules/nf-core/bedtools/shift/** - bedtools/slop: - modules/nf-core/bedtools/slop/** - tests/modules/nf-core/bedtools/slop/** - bedtools/sort: - modules/nf-core/bedtools/sort/** - tests/modules/nf-core/bedtools/sort/** - bedtools/split: - modules/nf-core/bedtools/split/** - tests/modules/nf-core/bedtools/split/** - bedtools/subtract: - modules/nf-core/bedtools/subtract/** - tests/modules/nf-core/bedtools/subtract/** - bedtools/unionbedg: - modules/nf-core/bedtools/unionbedg/** - tests/modules/nf-core/bedtools/unionbedg/** - bioawk: - modules/nf-core/bioawk/** - tests/modules/nf-core/bioawk/** - biobambam/bammarkduplicates2: - modules/nf-core/biobambam/bammarkduplicates2/** - tests/modules/nf-core/biobambam/bammarkduplicates2/** - biobambam/bammerge: - modules/nf-core/biobambam/bammerge/** - tests/modules/nf-core/biobambam/bammerge/** - biobambam/bamsormadup: - modules/nf-core/biobambam/bamsormadup/** - tests/modules/nf-core/biobambam/bamsormadup/** - biohansel: - modules/nf-core/biohansel/** - tests/modules/nf-core/biohansel/** - biscuit/align: - modules/nf-core/biscuit/index/** - modules/nf-core/biscuit/align/** - tests/modules/nf-core/biscuit/align/** - biscuit/biscuitblaster: - modules/nf-core/biscuit/index/** - modules/nf-core/biscuit/biscuitblaster/** - tests/modules/nf-core/biscuit/biscuitblaster/** - biscuit/bsconv: - modules/nf-core/biscuit/index/** - modules/nf-core/biscuit/bsconv/** - tests/modules/nf-core/biscuit/bsconv/** - biscuit/epiread: - modules/nf-core/biscuit/index/** - modules/nf-core/biscuit/epiread/** - tests/modules/nf-core/biscuit/epiread/** - biscuit/index: - modules/nf-core/biscuit/index/** - tests/modules/nf-core/biscuit/index/** - biscuit/mergecg: - modules/nf-core/biscuit/index/** - modules/nf-core/biscuit/mergecg/** - tests/modules/nf-core/biscuit/mergecg/** - biscuit/pileup: - modules/nf-core/biscuit/index/** - modules/nf-core/biscuit/pileup/** - tests/modules/nf-core/biscuit/pileup/** - biscuit/qc: - modules/nf-core/biscuit/index/** - modules/nf-core/biscuit/qc/** - tests/modules/nf-core/biscuit/qc/** - biscuit/vcf2bed: - modules/nf-core/biscuit/vcf2bed/** - tests/modules/nf-core/biscuit/vcf2bed/** - blat: - modules/nf-core/blat/** - tests/modules/nf-core/blat/** - bowtie/align: - modules/nf-core/bowtie/align/** - modules/nf-core/bowtie/build/** - tests/modules/nf-core/bowtie/align/** - bowtie/build: - modules/nf-core/bowtie/build/** - tests/modules/nf-core/bowtie/build_test/** - bracken/bracken: - modules/nf-core/bracken/bracken/** - tests/modules/nf-core/bracken/bracken/** - bracken/combinebrackenoutputs: - modules/nf-core/bracken/combinebrackenoutputs/** - tests/modules/nf-core/bracken/combinebrackenoutputs/** - busco: - modules/nf-core/busco/** - tests/modules/nf-core/busco/** - bwamem2/index: - modules/nf-core/bwamem2/index/** - tests/modules/nf-core/bwamem2/index/** - bwameth/align: - modules/nf-core/bwameth/align/** - tests/modules/nf-core/bwameth/align/** - bwameth/index: - modules/nf-core/bwameth/index/** - tests/modules/nf-core/bwameth/index/** - cadd: - modules/nf-core/cadd/** - tests/modules/nf-core/cadd/** - calder2: - modules/nf-core/calder2/** - tests/modules/nf-core/calder2/** - canu: - modules/nf-core/canu/** - tests/modules/nf-core/canu/** - cdhit/cdhitest: - modules/nf-core/cdhit/cdhitest/** - tests/modules/nf-core/cdhit/cdhitest/** - cellpose: - modules/nf-core/cellpose/** - tests/modules/nf-core/cellpose/** - cellranger/count: - modules/nf-core/cellranger/count/** - tests/modules/nf-core/cellranger/count/** @@ -506,25 +383,20 @@ cellranger/count: - tests/modules/nf-core/cellranger/mkref/** - modules/nf-core/cellranger/mkgtf/** - tests/modules/nf-core/cellranger/mkgtf/** - cellranger/mkfastq: - modules/nf-core/cellranger/mkfastq/** - tests/modules/nf-core/cellranger/mkfastq/** - cellranger/mkgtf: - modules/nf-core/cellranger/mkgtf/** - tests/modules/nf-core/cellranger/mkgtf/** - cellranger/mkref: - modules/nf-core/cellranger/mkref/** - tests/modules/nf-core/cellranger/mkref/** - modules/nf-core/cellranger/mkgtf/** - tests/modules/nf-core/cellranger/mkgtf/** - cellranger/mkvdjref: - modules/nf-core/cellranger/mkvdjref/** - tests/modules/nf-core/cellranger/mkvdjref/** - cellranger/multi: - modules/nf-core/cellranger/mkgtf/** - tests/modules/nf-core/cellranger/mkgtf/** @@ -532,3306 +404,2479 @@ cellranger/multi: - tests/modules/nf-core/cellranger/mkgtf/** - modules/nf-core/cellranger/multi/** - tests/modules/nf-core/cellranger/multi/** - cellranger/vdj: - modules/nf-core/cellranger/vdj/** - tests/modules/nf-core/cellranger/vdj/** - cellrangeratac/count: - modules/nf-core/cellrangeratac/count/** - tests/modules/nf-core/cellrangeratac/count/** - modules/nf-core/cellrangeratac/mkref/** - tests/modules/nf-core/cellrangeratac/mkref/** - cellrangeratac/mkfastq: - modules/nf-core/cellrangeratac/mkfastq/** - tests/modules/nf-core/cellrangeratac/mkfastq/** - cellrangeratac/mkref: - modules/nf-core/cellrangeratac/mkref/** - tests/modules/nf-core/cellrangeratac/mkref/** - centrifuge/centrifuge: - modules/nf-core/centrifuge/centrifuge/** - tests/modules/nf-core/centrifuge/centrifuge/** - checkm/lineagewf: - modules/nf-core/checkm/lineagewf/** - tests/modules/nf-core/checkm/lineagewf/** - checkm/qa: - modules/nf-core/checkm/qa/** - tests/modules/nf-core/checkm/qa/** - checkv/downloaddatabase: - modules/nf-core/checkv/downloaddatabase/** - tests/modules/nf-core/checkv/downloaddatabase/** - checkv/endtoend: - modules/nf-core/checkv/endtoend/** - tests/modules/nf-core/checkv/endtoend/** - checkv/updatedatabase: - modules/nf-core/checkv/updatedatabase/** - tests/modules/nf-core/checkv/updatedatabase/** - -chewbbaca/createschema: - - modules/nf-core/chewbbaca/createschema/** - - tests/modules/nf-core/chewbbaca/createschema/** - chromap/chromap: - modules/nf-core/chromap/chromap/** - tests/modules/nf-core/chromap/chromap/** - chromap/index: - modules/nf-core/chromap/index/** - tests/modules/nf-core/chromap/index/** - chromograph: - modules/nf-core/chromograph/** - tests/modules/nf-core/chromograph/** - circexplorer2/annotate: - modules/nf-core/circexplorer2/annotate/** - tests/modules/nf-core/circexplorer2/annotate/** - circexplorer2/parse: - modules/nf-core/circexplorer2/parse/** - tests/modules/nf-core/circexplorer2/parse/** - clippy: - modules/nf-core/clippy/** - tests/modules/nf-core/clippy/** - clonalframeml: - modules/nf-core/clonalframeml/** - tests/modules/nf-core/clonalframeml/** - cmseq/polymut: - modules/nf-core/cmseq/polymut/** - tests/modules/nf-core/cmseq/polymut/** - cnvkit/access: - modules/nf-core/cnvkit/access/** - tests/modules/nf-core/cnvkit/access/** - cnvkit/antitarget: - modules/nf-core/cnvkit/antitarget/** - tests/modules/nf-core/cnvkit/antitarget/** - cnvkit/batch: - modules/nf-core/cnvkit/batch/** - tests/modules/nf-core/cnvkit/batch/** - cnvkit/call: - modules/nf-core/cnvkit/call/** - tests/modules/nf-core/cnvkit/call/** - cnvkit/export: - modules/nf-core/cnvkit/export/** - tests/modules/nf-core/cnvkit/export/** - cnvkit/genemetrics: - modules/nf-core/cnvkit/genemetrics/** - tests/modules/nf-core/cnvkit/genemetrics/** - cnvkit/reference: - modules/nf-core/cnvkit/reference/** - tests/modules/nf-core/cnvkit/reference/** - cnvkit/target: - modules/nf-core/cnvkit/target/** - tests/modules/nf-core/cnvkit/target/** - cnvnator/cnvnator: - modules/nf-core/cnvnator/cnvnator/** - tests/modules/nf-core/cnvnator/cnvnator/** - cnvnator/convert2vcf: - modules/nf-core/cnvnator/convert2vcf/** - tests/modules/nf-core/cnvnator/convert2vcf/** - concoct/concoct: - modules/nf-core/concoct/concoct/** - tests/modules/nf-core/concoct/concoct/** - concoct/concoctcoveragetable: - modules/nf-core/concoct/concoctcoveragetable/** - tests/modules/nf-core/concoct/concoctcoveragetable/** - concoct/cutupfasta: - modules/nf-core/concoct/cutupfasta/** - tests/modules/nf-core/concoct/cutupfasta/** - concoct/extractfastabins: - modules/nf-core/concoct/extractfastabins/** - tests/modules/nf-core/concoct/extractfastabins/** - concoct/mergecutupclustering: - modules/nf-core/concoct/mergecutupclustering/** - tests/modules/nf-core/concoct/mergecutupclustering/** - conifer: - modules/nf-core/conifer/** - tests/modules/nf-core/conifer/** - controlfreec/assesssignificance: - modules/nf-core/controlfreec/assesssignificance/** - tests/modules/nf-core/controlfreec/assesssignificance/** - controlfreec/freec: - modules/nf-core/controlfreec/freec/** - tests/modules/nf-core/controlfreec/freec/** - controlfreec/freec2bed: - modules/nf-core/controlfreec/freec2bed/** - tests/modules/nf-core/controlfreec/freec2bed/** - controlfreec/freec2circos: - modules/nf-core/controlfreec/freec2circos/** - tests/modules/nf-core/controlfreec/freec2circos/** - controlfreec/makegraph: - modules/nf-core/controlfreec/makegraph/** - tests/modules/nf-core/controlfreec/makegraph/** - controlfreec/makegraph2: - modules/nf-core/controlfreec/makegraph2/** - tests/modules/nf-core/controlfreec/makegraph2/** - cooler/balance: - modules/nf-core/cooler/balance/** - tests/modules/nf-core/cooler/balance/** - cooler/cload: - modules/nf-core/cooler/cload/** - tests/modules/nf-core/cooler/cload/** - cooler/digest: - modules/nf-core/cooler/digest/** - tests/modules/nf-core/cooler/digest/** - cooler/dump: - modules/nf-core/cooler/dump/** - tests/modules/nf-core/cooler/dump/** - cooler/makebins: - modules/nf-core/cooler/makebins/** - tests/modules/nf-core/cooler/makebins/** - cooler/merge: - modules/nf-core/cooler/merge/** - tests/modules/nf-core/cooler/merge/** - cooler/zoomify: - modules/nf-core/cooler/zoomify/** - tests/modules/nf-core/cooler/zoomify/** - coreograph: - modules/nf-core/coreograph/** - tests/modules/nf-core/coreograph/** - crisprcleanr/normalize: - modules/nf-core/crisprcleanr/normalize/** - tests/modules/nf-core/crisprcleanr/normalize/** - crumble: - modules/nf-core/crumble/** - tests/modules/nf-core/crumble/** - csvtk/concat: - modules/nf-core/csvtk/concat/** - tests/modules/nf-core/csvtk/concat/** - csvtk/join: - modules/nf-core/csvtk/join/** - tests/modules/nf-core/csvtk/join/** - csvtk/split: - modules/nf-core/csvtk/split/** - tests/modules/nf-core/csvtk/split/** - custom/matrixfilter: - modules/nf-core/custom/matrixfilter/** - tests/modules/nf-core/custom/matrixfilter/** - custom/tabulartogseacls: - modules/nf-core/custom/tabulartogseacls/** - tests/modules/nf-core/custom/tabulartogseacls/** - custom/tabulartogseagct: - modules/nf-core/custom/tabulartogseagct/** - tests/modules/nf-core/custom/tabulartogseagct/** - cutesv: - modules/nf-core/cutesv/** - tests/modules/nf-core/cutesv/** - damageprofiler: - modules/nf-core/damageprofiler/** - tests/modules/nf-core/damageprofiler/** - dastool/dastool: - modules/nf-core/dastool/dastool/** - tests/modules/nf-core/dastool/dastool/** - dastool/fastatocontig2bin: - modules/nf-core/dastool/fastatocontig2bin/** - tests/modules/nf-core/dastool/fastatocontig2bin/** - dastool/scaffolds2bin: - modules/nf-core/dastool/scaffolds2bin/** - tests/modules/nf-core/dastool/scaffolds2bin/** - dedup: - modules/nf-core/dedup/** - tests/modules/nf-core/dedup/** - deeparg/downloaddata: - modules/nf-core/deeparg/downloaddata/** - tests/modules/nf-core/deeparg/downloaddata/** - deeparg/predict: - modules/nf-core/deeparg/predict/** - tests/modules/nf-core/deeparg/predict/** - deepbgc/download: - modules/nf-core/deepbgc/download/** - tests/modules/nf-core/deepbgc/download/** - deepbgc/pipeline: - modules/nf-core/deepbgc/pipeline/** - tests/modules/nf-core/deepbgc/pipeline/** - deepcell/mesmer: - modules/nf-core/deepcell/mesmer/** - tests/modules/nf-core/deepcell/mesmer/** - deeptmhmm: - modules/nf-core/deeptmhmm/** - tests/modules/nf-core/deeptmhmm/** - deeptools/bamcoverage: - modules/nf-core/deeptools/bamcoverage/** - tests/modules/nf-core/deeptools/bamcoverage/** - deeptools/computematrix: - modules/nf-core/deeptools/computematrix/** - tests/modules/nf-core/deeptools/computematrix/** - deeptools/multibamsummary: - modules/nf-core/deeptools/multibamsummary/** - tests/modules/nf-core/deeptools/multibamsummary/** - deeptools/plotcorrelation: - modules/nf-core/deeptools/plotcorrelation/** - tests/modules/nf-core/deeptools/plotcorrelation/** - deeptools/plotfingerprint: - modules/nf-core/deeptools/plotfingerprint/** - tests/modules/nf-core/deeptools/plotfingerprint/** - deeptools/plotheatmap: - modules/nf-core/deeptools/plotheatmap/** - tests/modules/nf-core/deeptools/plotheatmap/** - deeptools/plotpca: - modules/nf-core/deeptools/plotpca/** - tests/modules/nf-core/deeptools/plotpca/** - deeptools/plotprofile: - modules/nf-core/deeptools/plotprofile/** - tests/modules/nf-core/deeptools/plotprofile/** - deepvariant: - modules/nf-core/deepvariant/** - tests/modules/nf-core/deepvariant/** - delly/call: - modules/nf-core/delly/call/** - tests/modules/nf-core/delly/call/** - deseq2/differential: - modules/nf-core/deseq2/differential/** - tests/modules/nf-core/deseq2/differential/** - dragmap/align: - modules/nf-core/dragmap/align/** - tests/modules/nf-core/dragmap/align/** - dragmap/hashtable: - modules/nf-core/dragmap/hashtable/** - tests/modules/nf-core/dragmap/hashtable/** - dshbio/exportsegments: - modules/nf-core/dshbio/exportsegments/** - tests/modules/nf-core/dshbio/exportsegments/** - dshbio/filterbed: - modules/nf-core/dshbio/filterbed/** - tests/modules/nf-core/dshbio/filterbed/** - dshbio/filtergff3: - modules/nf-core/dshbio/filtergff3/** - tests/modules/nf-core/dshbio/filtergff3/** - dshbio/splitbed: - modules/nf-core/dshbio/splitbed/** - tests/modules/nf-core/dshbio/splitbed/** - dshbio/splitgff3: - modules/nf-core/dshbio/splitgff3/** - tests/modules/nf-core/dshbio/splitgff3/** - duphold: - modules/nf-core/duphold/** - tests/modules/nf-core/duphold/** - ectyper: - modules/nf-core/ectyper/** - tests/modules/nf-core/ectyper/** - eido/convert: - modules/nf-core/eido/convert/** - tests/modules/nf-core/eido/convert/** - eido/validate: - modules/nf-core/eido/validate/** - tests/modules/nf-core/eido/validate/** - eigenstratdatabasetools/eigenstratsnpcoverage: - modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/** - tests/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/** - elprep/filter: - modules/nf-core/elprep/filter/** - tests/modules/nf-core/elprep/filter/** - elprep/merge: - modules/nf-core/elprep/merge/** - tests/modules/nf-core/elprep/merge/** - elprep/split: - modules/nf-core/elprep/split/** - tests/modules/nf-core/elprep/split/** - emboss/cons: - modules/nf-core/emboss/cons/** - tests/modules/nf-core/emboss/cons/** - emboss/revseq: - modules/nf-core/emboss/revseq/** - tests/modules/nf-core/emboss/revseq/** - emboss/seqret: - modules/nf-core/emboss/seqret/** - tests/modules/nf-core/emboss/seqret/** - emmtyper: - modules/nf-core/emmtyper/** - tests/modules/nf-core/emmtyper/** - endorspy: - modules/nf-core/endorspy/** - tests/modules/nf-core/endorspy/** - ensemblvep/download: - modules/nf-core/ensemblvep/download/** - tests/modules/nf-core/ensemblvep/download/** - ensemblvep/filtervep: - modules/nf-core/ensemblvep/filtervep/** - tests/modules/nf-core/ensemblvep/filtervep/** - ensemblvep/vep: - modules/nf-core/ensemblvep/vep/** - tests/modules/nf-core/ensemblvep/vep/** - entrezdirect/esearch: - modules/nf-core/entrezdirect/esearch/** - tests/modules/nf-core/entrezdirect/esearch/** - entrezdirect/esummary: - modules/nf-core/entrezdirect/esummary/** - tests/modules/nf-core/entrezdirect/esummary/** - entrezdirect/xtract: - modules/nf-core/entrezdirect/xtract/** - tests/modules/nf-core/entrezdirect/xtract/** - epang/place: - modules/nf-core/epang/place/** - tests/modules/nf-core/epang/place/ - epang/split: - modules/nf-core/epang/split/** - tests/modules/nf-core/epang/split/** - estsfs: - modules/nf-core/estsfs/** - tests/modules/nf-core/estsfs/** - expansionhunter: - modules/nf-core/expansionhunter/** - tests/modules/nf-core/expansionhunter/** - expansionhunterdenovo/merge: - modules/nf-core/expansionhunterdenovo/merge/** - tests/modules/nf-core/expansionhunterdenovo/merge/** - expansionhunterdenovo/profile: - modules/nf-core/expansionhunterdenovo/profile/** - tests/modules/nf-core/expansionhunterdenovo/profile/** - falco: - modules/nf-core/falco/** - tests/modules/nf-core/falco/** - famsa/guidetree: - modules/nf-core/famsa/guidetree/** - tests/modules/nf-core/famsa/guidetree/** - faqcs: - modules/nf-core/faqcs/** - tests/modules/nf-core/faqcs/** - fastawindows: - modules/nf-core/fastawindows/** - tests/modules/nf-core/fastawindows/** - fastk/fastk: - modules/nf-core/fastk/fastk/** - tests/modules/nf-core/fastk/fastk/** - fastk/histex: - modules/nf-core/fastk/histex/** - tests/modules/nf-core/fastk/histex/** - fastk/merge: - modules/nf-core/fastk/merge/** - tests/modules/nf-core/fastk/merge/** - fasttree: - modules/nf-core/fasttree/** - tests/modules/nf-core/fasttree/** - fcs/fcsadaptor: - modules/nf-core/fcs/fcsadaptor/** - tests/modules/nf-core/fcs/fcsadaptor/** - fcs/fcsgx: - modules/nf-core/fcs/fcsgx/** - tests/modules/nf-core/fcs/fcsgx/** - ffq: - modules/nf-core/ffq/** - tests/modules/nf-core/ffq/** - fgbio/callduplexconsensusreads: - modules/nf-core/fgbio/callduplexconsensusreads/** - tests/modules/nf-core/fgbio/callduplexconsensusreads/** - fgbio/callmolecularconsensusreads: - modules/nf-core/fgbio/callmolecularconsensusreads/** - tests/modules/nf-core/fgbio/callmolecularconsensusreads/** - fgbio/filterconsensusreads: - modules/nf-core/fgbio/filterconsensusreads/** - tests/modules/nf-core/fgbio/filterconsensusreads/** - fgbio/groupreadsbyumi: - modules/nf-core/fgbio/groupreadsbyumi/** - tests/modules/nf-core/fgbio/groupreadsbyumi/** - fgbio/sortbam: - modules/nf-core/fgbio/sortbam/** - tests/modules/nf-core/fgbio/sortbam/** - fgbio/zipperbams: - modules/nf-core/fgbio/zipperbams/** - tests/modules/nf-core/fgbio/zipperbams/** - filtlong: - modules/nf-core/filtlong/** - tests/modules/nf-core/filtlong/** - flash: - modules/nf-core/flash/** - tests/modules/nf-core/flash/** - fqtk: - modules/nf-core/fqtk/** - modules/nf-core/untar/** - tests/modules/nf-core/fqtk/** - freebayes: - modules/nf-core/freebayes/** - tests/modules/nf-core/freebayes/** - freyja/boot: - modules/nf-core/freyja/boot/** - tests/modules/nf-core/freyja/boot/** - freyja/demix: - modules/nf-core/freyja/demix/** - tests/modules/nf-core/freyja/demix/** - freyja/update: - modules/nf-core/freyja/update/** - tests/modules/nf-core/freyja/update/** - freyja/variants: - modules/nf-core/freyja/variants/** - tests/modules/nf-core/freyja/variants/** - galah: - modules/nf-core/galah/** - tests/modules/nf-core/galah/** - gamma/gamma: - modules/nf-core/gamma/gamma/** - tests/modules/nf-core/gamma/gamma/** - gangstr: - modules/nf-core/gangstr/** - tests/modules/nf-core/gangstr/** - ganon/buildcustom: - modules/nf-core/ganon/buildcustom/** - tests/modules/nf-core/ganon/buildcustom/** - ganon/classify: - modules/nf-core/ganon/classify/** - tests/modules/nf-core/ganon/classify/** - ganon/report: - modules/nf-core/ganon/report/** - tests/modules/nf-core/ganon/report/** - ganon/table: - modules/nf-core/ganon/table/** - tests/modules/nf-core/ganon/table/** - gappa/examineassign: - modules/nf-core/gappa/examineassign/** - tests/modules/nf-core/gappa/examineassign/** - gappa/examinegraft: - modules/nf-core/gappa/examinegraft/** - tests/modules/nf-core/gappa/examinegraft/** - gappa/examineheattree: - modules/nf-core/gappa/examineheattree/** - tests/modules/nf-core/gappa/examineheattree/** - gatk/indelrealigner: - modules/nf-core/gatk/indelrealigner/** - tests/modules/nf-core/gatk/indelrealigner/** - gatk/realignertargetcreator: - modules/nf-core/gatk/realignertargetcreator/** - tests/modules/nf-core/gatk/realignertargetcreator/** - gatk/unifiedgenotyper: - modules/nf-core/gatk/unifiedgenotyper/** - tests/modules/nf-core/gatk/unifiedgenotyper/** - gatk4/annotateintervals: - modules/nf-core/gatk4/annotateintervals/** - tests/modules/nf-core/gatk4/annotateintervals/** - gatk4/applybqsr: - modules/nf-core/gatk4/applybqsr/** - tests/modules/nf-core/gatk4/applybqsr/** - gatk4/applyvqsr: - modules/nf-core/gatk4/applyvqsr/** - tests/modules/nf-core/gatk4/applyvqsr/** - gatk4/asereadcounter: - modules/nf-core/gatk4/asereadcounter/** - tests/modules/nf-core/gatk4/asereadcounter/** - gatk4/baserecalibrator: - modules/nf-core/gatk4/baserecalibrator/** - tests/modules/nf-core/gatk4/baserecalibrator/** - gatk4/bedtointervallist: - modules/nf-core/gatk4/bedtointervallist/** - tests/modules/nf-core/gatk4/bedtointervallist/** - gatk4/calculatecontamination: - modules/nf-core/gatk4/calculatecontamination/** - tests/modules/nf-core/gatk4/calculatecontamination/** - gatk4/calibratedragstrmodel: - modules/nf-core/gatk4/calibratedragstrmodel/** - tests/modules/nf-core/gatk4/calibratedragstrmodel/** - gatk4/cnnscorevariants: - modules/nf-core/gatk4/cnnscorevariants/** - tests/modules/nf-core/gatk4/cnnscorevariants/** - gatk4/collectreadcounts: - modules/nf-core/gatk4/collectreadcounts/** - tests/modules/nf-core/gatk4/collectreadcounts/** - gatk4/collectsvevidence: - modules/nf-core/gatk4/collectsvevidence/** - tests/modules/nf-core/gatk4/collectsvevidence/** - gatk4/combinegvcfs: - modules/nf-core/gatk4/combinegvcfs/** - tests/modules/nf-core/gatk4/combinegvcfs/** - gatk4/composestrtablefile: - modules/nf-core/gatk4/composestrtablefile/** - tests/modules/nf-core/gatk4/composestrtablefile/** - gatk4/condensedepthevidence: - modules/nf-core/gatk4/condensedepthevidence/** - tests/modules/nf-core/gatk4/condensedepthevidence/** - gatk4/createreadcountpanelofnormals: - modules/nf-core/gatk4/createreadcountpanelofnormals/** - tests/modules/nf-core/gatk4/createreadcountpanelofnormals/** - gatk4/createsequencedictionary: - modules/nf-core/gatk4/createsequencedictionary/** - tests/modules/nf-core/gatk4/createsequencedictionary/** - gatk4/createsomaticpanelofnormals: - modules/nf-core/gatk4/createsomaticpanelofnormals/** - tests/modules/nf-core/gatk4/createsomaticpanelofnormals/** - gatk4/denoisereadcounts: - modules/nf-core/gatk4/denoisereadcounts/** - tests/modules/nf-core/gatk4/denoisereadcounts/** - gatk4/determinegermlinecontigploidy: - modules/nf-core/gatk4/determinegermlinecontigploidy/** - tests/modules/nf-core/gatk4/determinegermlinecontigploidy/** - gatk4/estimatelibrarycomplexity: - modules/nf-core/gatk4/estimatelibrarycomplexity/** - tests/modules/nf-core/gatk4/estimatelibrarycomplexity/** - gatk4/fastqtosam: - modules/nf-core/gatk4/fastqtosam/** - tests/modules/nf-core/gatk4/fastqtosam/** - gatk4/filterintervals: - modules/nf-core/gatk4/filterintervals/** - tests/modules/nf-core/gatk4/filterintervals/** - gatk4/filtermutectcalls: - modules/nf-core/gatk4/filtermutectcalls/** - tests/modules/nf-core/gatk4/filtermutectcalls/** - gatk4/filtervarianttranches: - modules/nf-core/gatk4/filtervarianttranches/** - tests/modules/nf-core/gatk4/filtervarianttranches/** - gatk4/gatherbqsrreports: - modules/nf-core/gatk4/gatherbqsrreports/** - tests/modules/nf-core/gatk4/gatherbqsrreports/** - gatk4/gatherpileupsummaries: - modules/nf-core/gatk4/gatherpileupsummaries/** - tests/modules/nf-core/gatk4/gatherpileupsummaries/** - gatk4/genomicsdbimport: - modules/nf-core/gatk4/genomicsdbimport/** - tests/modules/nf-core/gatk4/genomicsdbimport/** - gatk4/genotypegvcfs: - modules/nf-core/gatk4/genotypegvcfs/** - tests/modules/nf-core/gatk4/genotypegvcfs/** - gatk4/germlinecnvcaller: - modules/nf-core/gatk4/germlinecnvcaller/** - tests/modules/nf-core/gatk4/germlinecnvcaller/** - gatk4/getpileupsummaries: - modules/nf-core/gatk4/getpileupsummaries/** - tests/modules/nf-core/gatk4/getpileupsummaries/** - gatk4/indexfeaturefile: - modules/nf-core/gatk4/indexfeaturefile/** - tests/modules/nf-core/gatk4/indexfeaturefile/** - gatk4/intervallisttobed: - modules/nf-core/gatk4/intervallisttobed/** - tests/modules/nf-core/gatk4/intervallisttobed/** - gatk4/intervallisttools: - modules/nf-core/gatk4/intervallisttools/** - tests/modules/nf-core/gatk4/intervallisttools/** - gatk4/learnreadorientationmodel: - modules/nf-core/gatk4/learnreadorientationmodel/** - tests/modules/nf-core/gatk4/learnreadorientationmodel/** - gatk4/leftalignandtrimvariants: - modules/nf-core/gatk4/leftalignandtrimvariants/** - tests/modules/nf-core/gatk4/leftalignandtrimvariants/** - gatk4/markduplicates: - modules/nf-core/gatk4/markduplicates/** - tests/modules/nf-core/gatk4/markduplicates/** - gatk4/mergebamalignment: - modules/nf-core/gatk4/mergebamalignment/** - tests/modules/nf-core/gatk4/mergebamalignment/** - gatk4/mergemutectstats: - modules/nf-core/gatk4/mergemutectstats/** - tests/modules/nf-core/gatk4/mergemutectstats/** - gatk4/mergevcfs: - modules/nf-core/gatk4/mergevcfs/** - tests/modules/nf-core/gatk4/mergevcfs/** - gatk4/mutect2: - modules/nf-core/gatk4/mutect2/** - tests/modules/nf-core/gatk4/mutect2/** - gatk4/postprocessgermlinecnvcalls: - modules/nf-core/gatk4/postprocessgermlinecnvcalls/** - tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/** - gatk4/preprocessintervals: - modules/nf-core/gatk4/preprocessintervals/** - tests/modules/nf-core/gatk4/preprocessintervals/** - gatk4/printreads: - modules/nf-core/gatk4/printreads/** - tests/modules/nf-core/gatk4/printreads/** - gatk4/printsvevidence: - modules/nf-core/gatk4/printsvevidence/** - tests/modules/nf-core/gatk4/printsvevidence/** - gatk4/reblockgvcf: - modules/nf-core/gatk4/reblockgvcf/** - tests/modules/nf-core/gatk4/reblockgvcf/** - gatk4/revertsam: - modules/nf-core/gatk4/revertsam/** - tests/modules/nf-core/gatk4/revertsam/** - gatk4/samtofastq: - modules/nf-core/gatk4/samtofastq/** - tests/modules/nf-core/gatk4/samtofastq/** - gatk4/selectsamples: - modules/nf-core/gatk4/selectsamples/** - tests/modules/nf-core/gatk4/selectsamples/** - gatk4/selectvariants: - modules/nf-core/gatk4/selectvariants/** - tests/modules/nf-core/gatk4/selectvariants/** - gatk4/shiftfasta: - modules/nf-core/gatk4/shiftfasta/** - tests/modules/nf-core/gatk4/shiftfasta/** - gatk4/sitedepthtobaf: - modules/nf-core/gatk4/sitedepthtobaf/** - tests/modules/nf-core/gatk4/sitedepthtobaf/** - gatk4/splitcram: - modules/nf-core/gatk4/splitcram/** - tests/modules/nf-core/gatk4/splitcram/** - gatk4/splitintervals: - modules/nf-core/gatk4/splitintervals/** - tests/modules/nf-core/gatk4/splitintervals/** - gatk4/splitncigarreads: - modules/nf-core/gatk4/splitncigarreads/** - tests/modules/nf-core/gatk4/splitncigarreads/** - gatk4/svannotate: - modules/nf-core/gatk4/svannotate/** - tests/modules/nf-core/gatk4/svannotate/** - gatk4/svcluster: - modules/nf-core/gatk4/svcluster/** - tests/modules/nf-core/gatk4/svcluster/** - gatk4/variantfiltration: - modules/nf-core/gatk4/variantfiltration/** - tests/modules/nf-core/gatk4/variantfiltration/** - gatk4/variantrecalibrator: - modules/nf-core/gatk4/variantrecalibrator/** - tests/modules/nf-core/gatk4/variantrecalibrator/** - gatk4spark/applybqsr: - modules/nf-core/gatk4spark/applybqsr/** - tests/modules/nf-core/gatk4spark/applybqsr/** - gatk4spark/baserecalibrator: - modules/nf-core/gatk4spark/baserecalibrator/** - tests/modules/nf-core/gatk4spark/baserecalibrator/** - gatk4spark/markduplicates: - modules/nf-core/gatk4spark/markduplicates/** - tests/modules/nf-core/gatk4spark/markduplicates/** - gawk: - modules/nf-core/gawk/** - tests/modules/nf-core/gawk/** - gecco/run: - modules/nf-core/gecco/run/** - tests/modules/nf-core/gecco/run/** - gem2/gem2bedmappability: - modules/nf-core/gem2/gem2bedmappability/** - tests/modules/nf-core/gem2/gem2bedmappability/** - gem2/gemindexer: - modules/nf-core/gem2/gemindexer/** - tests/modules/nf-core/gem2/gemindexer/** - gem2/gemmappability: - modules/nf-core/gem2/gemmappability/** - tests/modules/nf-core/gem2/gemmappability/** - gem3/gem3indexer: - modules/nf-core/gem3/gem3indexer/** - tests/modules/nf-core/gem3/gem3indexer/** - genescopefk: - modules/nf-core/genescopefk/** - tests/modules/nf-core/genescopefk/** - genmap/index: - modules/nf-core/genmap/index/** - tests/modules/nf-core/genmap/index/** - genmap/map: - modules/nf-core/genmap/map/** - tests/modules/nf-core/genmap/map/** - genmod/annotate: - modules/nf-core/genmod/annotate/** - tests/modules/nf-core/genmod/annotate/** - genmod/compound: - modules/nf-core/genmod/compound/** - tests/modules/nf-core/genmod/compound/** - genmod/models: - modules/nf-core/genmod/models/** - tests/modules/nf-core/genmod/models/** - genmod/score: - modules/nf-core/genmod/score/** - tests/modules/nf-core/genmod/score/** - genomad/download: - modules/nf-core/genomad/download/** - tests/modules/nf-core/genomad/download/** - genomad/endtoend: - modules/nf-core/genomad/endtoend/** - tests/modules/nf-core/genomad/endtoend/** - genomescope2: - modules/nf-core/genomescope2/** - tests/modules/nf-core/genomescope2/** - genotyphi/parse: - modules/nf-core/genotyphi/parse/** - tests/modules/nf-core/genotyphi/parse/** - genrich: - modules/nf-core/genrich/** - tests/modules/nf-core/genrich/** - geoquery/getgeo: - modules/nf-core/geoquery/getgeo/** - tests/modules/nf-core/geoquery/getgeo/** - gfaffix: - modules/nf-core/gfaffix/** - tests/modules/nf-core/gfaffix/** - gfastats: - modules/nf-core/gfastats/** - tests/modules/nf-core/gfastats/** - gfatools/gfa2fa: - modules/nf-core/gfatools/gfa2fa/** - tests/modules/nf-core/gfatools/gfa2fa/** - gfatools/stat: - modules/nf-core/gfatools/stat/** - tests/modules/nf-core/gfatools/stat/** - gffcompare: - modules/nf-core/gffcompare/** - tests/modules/nf-core/gffcompare/** - gget/gget: - modules/nf-core/gget/gget/** - tests/modules/nf-core/gget/gget/** - glimpse2/chunk: - modules/nf-core/glimpse2/chunk/** - tests/modules/nf-core/glimpse2/chunk/** - glimpse2/concordance: - modules/nf-core/glimpse2/concordance/** - tests/modules/nf-core/glimpse2/concordance/** - glimpse2/ligate: - modules/nf-core/glimpse2/ligate/** - tests/modules/nf-core/glimpse2/ligate/** - glimpse2/splitreference: - modules/nf-core/glimpse2/splitreference/** - tests/modules/nf-core/glimpse2/splitreference/** - glnexus: - modules/nf-core/glnexus/** - tests/modules/nf-core/glnexus/** - gnu/sort: - modules/nf-core/gnu/sort/** - tests/modules/nf-core/gnu/sort/** - goat/taxonsearch: - modules/nf-core/goat/taxonsearch/** - tests/modules/nf-core/goat/taxonsearch/** - goleft/indexcov: - modules/nf-core/goleft/indexcov/** - tests/modules/nf-core/goleft/indexcov/** - goleft/indexsplit: - modules/nf-core/goleft/indexsplit/** - tests/modules/nf-core/goleft/indexsplit/** - gprofiler2/gost: - modules/nf-core/gprofiler2/gost/** - tests/modules/nf-core/gprofiler2/gost/** - graphmap2/align: - modules/nf-core/graphmap2/align/** - tests/modules/nf-core/graphmap2/align/** - graphmap2/index: - modules/nf-core/graphmap2/index/** - tests/modules/nf-core/graphmap2/index/** - graphtyper/genotype: - modules/nf-core/graphtyper/genotype/** - tests/modules/nf-core/graphtyper/genotype/** - graphtyper/vcfconcatenate: - modules/nf-core/graphtyper/vcfconcatenate/** - tests/modules/nf-core/graphtyper/vcfconcatenate/** - grids/gridsssomaticfilter: - modules/nf-core/grids/gridsssomaticfilter/** - tests/modules/nf-core/grids/gridsssomaticfilter/** - gridss/gridss: - modules/nf-core/gridss/gridss/** - tests/modules/nf-core/gridss/gridss/** - gridss/gridssgenerateponbedpe: - modules/nf-core/gridss/gridssgenerateponbedpe/** - tests/modules/nf-core/gridss/gridssgenerateponbedpe/** - gsea/gsea: - modules/nf-core/gsea/gsea/** - tests/modules/nf-core/gsea/gsea/** - gstama/collapse: - modules/nf-core/gstama/collapse/** - tests/modules/nf-core/gstama/collapse/** - gstama/merge: - modules/nf-core/gstama/merge/** - tests/modules/nf-core/gstama/merge/** - gstama/polyacleanup: - modules/nf-core/gstama/polyacleanup/** - tests/modules/nf-core/gstama/polyacleanup/** - gtdbtk/classifywf: - modules/nf-core/gtdbtk/classifywf/** - tests/modules/nf-core/gtdbtk/classifywf/** - gubbins: - modules/nf-core/gubbins/** - tests/modules/nf-core/gubbins/** - gunc/downloaddb: - modules/nf-core/gunc/downloaddb/** - tests/modules/nf-core/gunc/downloaddb/** - gunc/mergecheckm: - modules/nf-core/gunc/mergecheckm/** - tests/modules/nf-core/gunc/mergecheckm/** - gunc/run: - modules/nf-core/gunc/run/** - tests/modules/nf-core/gunc/run/** - gvcftools/extractvariants: - modules/nf-core/gvcftools/extractvariants/** - tests/modules/nf-core/gvcftools/extractvariants/** - hamronization/abricate: - modules/nf-core/hamronization/abricate/** - tests/modules/nf-core/hamronization/abricate/** - hamronization/amrfinderplus: - modules/nf-core/hamronization/amrfinderplus/** - tests/modules/nf-core/hamronization/amrfinderplus/** - hamronization/deeparg: - modules/nf-core/hamronization/deeparg/** - tests/modules/nf-core/hamronization/deeparg/** - hamronization/fargene: - modules/nf-core/hamronization/fargene/** - tests/modules/nf-core/hamronization/fargene/** - hamronization/rgi: - modules/nf-core/hamronization/rgi/** - tests/modules/nf-core/hamronization/rgi/** - hamronization/summarize: - modules/nf-core/hamronization/summarize/** - tests/modules/nf-core/hamronization/summarize/** - hapibd: - modules/nf-core/hapibd/** - tests/modules/nf-core/hapibd/** - haplocheck: - modules/nf-core/haplocheck/** - tests/modules/nf-core/haplocheck/** - haplogrep2/classify: - modules/nf-core/haplogrep2/classify/** - tests/modules/nf-core/haplogrep2/classify/** - happy/happy: - modules/nf-core/happy/happy/** - tests/modules/nf-core/happy/happy/** - happy/prepy: - modules/nf-core/happy/prepy/** - tests/modules/nf-core/happy/prepy/** - happy/sompy: - modules/nf-core/happy/sompy/** - tests/modules/nf-core/happy/sompy/** - hicap: - modules/nf-core/hicap/** - tests/modules/nf-core/hicap/** - hicexplorer/hicpca: - modules/nf-core/hicexplorer/hicpca/** - tests/modules/nf-core/hicexplorer/hicpca/** - hifiasm: - modules/nf-core/hifiasm/** - tests/modules/nf-core/hifiasm/** - hlala/preparegraph: - modules/nf-core/hlala/preparegraph/** - tests/modules/nf-core/hlala/preparegraph/** - hlala/typing: - modules/nf-core/hlala/typing/** - tests/modules/nf-core/hlala/typing/** - hmmcopy/gccounter: - modules/nf-core/hmmcopy/gccounter/** - tests/modules/nf-core/hmmcopy/gccounter/** - hmmcopy/generatemap: - modules/nf-core/hmmcopy/generatemap/** - tests/modules/nf-core/hmmcopy/generatemap/** - hmmcopy/mapcounter: - modules/nf-core/hmmcopy/mapcounter/** - tests/modules/nf-core/hmmcopy/mapcounter/** - hmmcopy/readcounter: - modules/nf-core/hmmcopy/readcounter/** - tests/modules/nf-core/hmmcopy/readcounter/** - hmmer/eslalimask: - modules/nf-core/hmmer/eslalimask/** - tests/modules/nf-core/hmmer/eslalimask/** - hmmer/eslreformat: - modules/nf-core/hmmer/eslreformat/** - tests/modules/nf-core/hmmer/eslreformat/** - hmmer/hmmalign: - modules/nf-core/hmmer/hmmalign/** - tests/modules/nf-core/hmmer/hmmalign/** - hmmer/hmmbuild: - modules/nf-core/hmmer/hmmbuild/** - tests/modules/nf-core/hmmer/hmmbuild/** - hmmer/hmmfetch: - modules/nf-core/hmmer/hmmfetch/** - tests/modules/nf-core/hmmer/hmmfetch/** - hmmer/hmmsearch: - modules/nf-core/hmmer/hmmsearch/** - tests/modules/nf-core/hmmer/hmmsearch/** - hmtnote/annotate: - modules/nf-core/hmtnote/annotate/** - tests/modules/nf-core/hmtnote/annotate/** - homer/annotatepeaks: - modules/nf-core/homer/annotatepeaks/** - tests/modules/nf-core/homer/annotatepeaks/** - homer/findpeaks: - modules/nf-core/homer/findpeaks/** - modules/nf-core/homer/maketagdirectory/** - tests/modules/nf-core/homer/findpeaks/** - homer/maketagdirectory: - modules/nf-core/homer/maketagdirectory/** - tests/modules/nf-core/homer/maketagdirectory/** - homer/makeucscfile: - modules/nf-core/homer/makeucscfile/** - tests/modules/nf-core/homer/makeucscfile/** - homer/pos2bed: - modules/nf-core/homer/pos2bed/** - modules/nf-core/homer/maketagdirectory/** - modules/nf-core/homer/findpeaks/** - tests/modules/nf-core/homer/pos2bed/** - hpsuissero: - modules/nf-core/hpsuissero/** - tests/modules/nf-core/hpsuissero/** - htseq/count: - modules/nf-core/htseq/count/** - tests/modules/nf-core/htseq/count/** - hypo: - modules/nf-core/hypo/** - tests/modules/nf-core/hypo/** - ichorcna/createpon: - modules/nf-core/ichorcna/createpon/** - tests/modules/nf-core/ichorcna/createpon/** - ichorcna/run: - modules/nf-core/ichorcna/run/** - tests/modules/nf-core/ichorcna/run/** - icountmini/metagene: - modules/nf-core/icountmini/metagene/** - tests/modules/nf-core/icountmini/metagene/** - icountmini/peaks: - modules/nf-core/icountmini/peaks/** - tests/modules/nf-core/icountmini/peaks/** - icountmini/segment: - modules/nf-core/icountmini/segment/** - tests/modules/nf-core/icountmini/segment/** - icountmini/sigxls: - modules/nf-core/icountmini/sigxls/** - tests/modules/nf-core/icountmini/sigxls/** - icountmini/summary: - modules/nf-core/icountmini/summary/** - tests/modules/nf-core/icountmini/summary/** - idr: - modules/nf-core/idr/** - tests/modules/nf-core/idr/** - igv/js: - modules/nf-core/igv/js/** - tests/modules/nf-core/igv/js/** - ilastik/multicut: - modules/nf-core/ilastik/multicut/** - tests/modules/nf-core/ilastik/multicut/** - ilastik/pixelclassification: - modules/nf-core/ilastik/pixelclassification/** - tests/modules/nf-core/ilastik/pixelclassification/** - instrain/compare: - modules/nf-core/instrain/compare/** - tests/modules/nf-core/instrain/compare/** - instrain/profile: - modules/nf-core/instrain/profile/** - tests/modules/nf-core/instrain/profile/** - iphop/addtodb: - modules/nf-core/iphop/addtodb/** - tests/modules/nf-core/iphop/addtodb/** - iphop/download: - modules/nf-core/iphop/download/** - tests/modules/nf-core/iphop/download/** - iphop/predict: - modules/nf-core/iphop/predict/** - tests/modules/nf-core/iphop/predict/** - iqtree: - modules/nf-core/iqtree/** - tests/modules/nf-core/iqtree/** - islandpath: - modules/nf-core/islandpath/** - tests/modules/nf-core/islandpath/** - ismapper: - modules/nf-core/ismapper/** - tests/modules/nf-core/ismapper/** - isoseq3/cluster: - modules/nf-core/isoseq3/cluster/** - tests/modules/nf-core/isoseq3/cluster/** - isoseq3/refine: - modules/nf-core/isoseq3/refine/** - tests/modules/nf-core/isoseq3/refine/** - ivar/consensus: - modules/nf-core/ivar/consensus/** - tests/modules/nf-core/ivar/consensus/** - ivar/trim: - modules/nf-core/ivar/trim/** - tests/modules/nf-core/ivar/trim/** - ivar/variants: - modules/nf-core/ivar/variants/** - tests/modules/nf-core/ivar/variants/** - jasminesv: - modules/nf-core/jasminesv/** - tests/modules/nf-core/jasminesv/** - jupyternotebook: - modules/nf-core/jupyternotebook/** - tests/modules/nf-core/jupyternotebook/** - kaiju/kaiju: - modules/nf-core/kaiju/kaiju/** - tests/modules/nf-core/kaiju/kaiju/** - kaiju/kaiju2krona: - modules/nf-core/kaiju/kaiju2krona/** - tests/modules/nf-core/kaiju/kaiju2krona/** - kaiju/kaiju2table: - modules/nf-core/kaiju/kaiju2table/** - tests/modules/nf-core/kaiju/kaiju2table/** - kaiju/mkfmi: - modules/nf-core/kaiju/mkfmi/** - tests/modules/nf-core/kaiju/mkfmi/** - kallistobustools/count: - modules/nf-core/kallistobustools/count/** - tests/modules/nf-core/kallistobustools/count/** - kallistobustools/ref: - modules/nf-core/kallistobustools/ref/** - tests/modules/nf-core/kallistobustools/ref/** - kat/hist: - modules/nf-core/kat/hist/** - tests/modules/nf-core/kat/hist/** - khmer/normalizebymedian: - modules/nf-core/khmer/normalizebymedian/** - tests/modules/nf-core/khmer/normalizebymedian/** - khmer/uniquekmers: - modules/nf-core/khmer/uniquekmers/** - tests/modules/nf-core/khmer/uniquekmers/** - kleborate: - modules/nf-core/kleborate/** - tests/modules/nf-core/kleborate/** - kmcp/compute: - modules/nf-core/kmcp/compute/** - tests/modules/nf-core/kmcp/compute/** - kmcp/index: - modules/nf-core/kmcp/index/** - tests/modules/nf-core/kmcp/index/** - kmcp/merge: - modules/nf-core/kmcp/merge/** - tests/modules/nf-core/kmcp/merge/** - kmcp/profile: - modules/nf-core/kmcp/profile/** - tests/modules/nf-core/kmcp/profile/** - kmcp/search: - modules/nf-core/kmcp/search/** - tests/modules/nf-core/kmcp/search/** - kofamscan: - modules/nf-core/kofamscan/** - tests/modules/nf-core/kofamscan/** - krakentools/combinekreports: - modules/nf-core/krakentools/combinekreports/** - tests/modules/nf-core/krakentools/combinekreports/** - krakentools/kreport2krona: - modules/nf-core/krakentools/kreport2krona/** - tests/modules/nf-core/krakentools/kreport2krona/** - krakenuniq/build: - modules/nf-core/krakenuniq/build/** - tests/modules/nf-core/krakenuniq/build/** - krakenuniq/download: - modules/nf-core/krakenuniq/download/** - tests/modules/nf-core/krakenuniq/download/** - krona/kronadb: - modules/nf-core/krona/kronadb/** - tests/modules/nf-core/krona/kronadb/** - krona/ktimporttaxonomy: - modules/nf-core/krona/ktimporttaxonomy/** - tests/modules/nf-core/krona/ktimporttaxonomy/** - krona/ktimporttext: - modules/nf-core/krona/ktimporttext/** - tests/modules/nf-core/krona/ktimporttext/** - krona/ktupdatetaxonomy: - modules/nf-core/krona/ktupdatetaxonomy/** - tests/modules/nf-core/krona/ktupdatetaxonomy/** - last/dotplot: - modules/nf-core/last/dotplot/** - tests/modules/nf-core/last/dotplot/** - last/lastal: - modules/nf-core/last/lastal/** - tests/modules/nf-core/last/lastal/** - last/lastdb: - modules/nf-core/last/lastdb/** - tests/modules/nf-core/last/lastdb/** - last/mafconvert: - modules/nf-core/last/mafconvert/** - tests/modules/nf-core/last/mafconvert/** - last/mafswap: - modules/nf-core/last/mafswap/** - tests/modules/nf-core/last/mafswap/** - last/postmask: - modules/nf-core/last/postmask/** - tests/modules/nf-core/last/postmask/** - last/split: - modules/nf-core/last/split/** - tests/modules/nf-core/last/split/** - last/train: - modules/nf-core/last/train/** - tests/modules/nf-core/last/train/** - leehom: - modules/nf-core/leehom/** - tests/modules/nf-core/leehom/** - legsta: - modules/nf-core/legsta/** - tests/modules/nf-core/legsta/** - lima: - modules/nf-core/lima/** - tests/modules/nf-core/lima/** - limma/differential: - modules/nf-core/limma/differential/** - tests/modules/nf-core/limma/differential/** - lissero: - modules/nf-core/lissero/** - tests/modules/nf-core/lissero/** - lofreq/call: - modules/nf-core/lofreq/call/** - tests/modules/nf-core/lofreq/call/** - lofreq/callparallel: - modules/nf-core/lofreq/callparallel/** - tests/modules/nf-core/lofreq/callparallel/** - lofreq/filter: - modules/nf-core/lofreq/filter/** - tests/modules/nf-core/lofreq/filter/** - lofreq/indelqual: - modules/nf-core/lofreq/indelqual/** - tests/modules/nf-core/lofreq/indelqual/** - lofreq/somatic: - modules/nf-core/lofreq/somatic/** - tests/modules/nf-core/lofreq/somatic/** - macrel/contigs: - modules/nf-core/macrel/contigs/** - tests/modules/nf-core/macrel/contigs/** - macs2/callpeak: - modules/nf-core/macs2/callpeak/** - tests/modules/nf-core/macs2/callpeak/** - mageck/count: - modules/nf-core/mageck/count/** - tests/modules/nf-core/mageck/count/** - mageck/mle: - modules/nf-core/mageck/mle/** - tests/modules/nf-core/mageck/mle/** - mageck/test: - modules/nf-core/mageck/test/** - tests/modules/nf-core/mageck/test/** - malt/build: - modules/nf-core/malt/build/** - tests/modules/nf-core/malt/build_test/** - malt/run: - modules/nf-core/malt/run/** - tests/modules/nf-core/malt/run/** - maltextract: - modules/nf-core/maltextract/** - tests/modules/nf-core/maltextract/** - manta/convertinversion: - modules/nf-core/manta/convertinversion/** - tests/modules/nf-core/manta/convertinversion/** - manta/germline: - modules/nf-core/manta/germline/** - tests/modules/nf-core/manta/germline/** - manta/somatic: - modules/nf-core/manta/somatic/** - tests/modules/nf-core/manta/somatic/** - manta/tumoronly: - modules/nf-core/manta/tumoronly/** - tests/modules/nf-core/manta/tumoronly/** - mapad/index: - modules/nf-core/mapad/index/** - tests/modules/nf-core/mapad/index/** - mapad/map: - modules/nf-core/mapad/map/** - tests/modules/nf-core/mapad/map/** - mapdamage2: - modules/nf-core/mapdamage2/** - tests/modules/nf-core/mapdamage2/** - mash/dist: - modules/nf-core/mash/dist/** - tests/modules/nf-core/mash/dist/** - mash/screen: - modules/nf-core/mash/screen/** - tests/modules/nf-core/mash/screen/** - mash/sketch: - modules/nf-core/mash/sketch/** - tests/modules/nf-core/mash/sketch/** - mashtree: - modules/nf-core/mashtree/** - tests/modules/nf-core/mashtree/** - maxbin2: - modules/nf-core/maxbin2/** - tests/modules/nf-core/maxbin2/** - maxquant/lfq: - modules/nf-core/maxquant/lfq/** - tests/modules/nf-core/maxquant/lfq/** - mcquant: - modules/nf-core/mcquant/** - tests/modules/nf-core/mcquant/** - mcroni: - modules/nf-core/mcroni/** - tests/modules/nf-core/mcroni/** - md5sum: - modules/nf-core/md5sum/** - tests/modules/nf-core/md5sum/** - megahit: - modules/nf-core/megahit/** - tests/modules/nf-core/megahit/** - megan/daa2info: - modules/nf-core/megan/daa2info/** - tests/modules/nf-core/megan/daa2info/** - megan/rma2info: - modules/nf-core/megan/rma2info/** - tests/modules/nf-core/megan/rma2info/** - melt: - modules/nf-core/melt/** - tests/modules/nf-core/melt/** - meningotype: - modules/nf-core/meningotype/** - tests/modules/nf-core/meningotype/** - merqury: - modules/nf-core/merqury/** - tests/modules/nf-core/merqury/** - merquryfk/katcomp: - modules/nf-core/merquryfk/katcomp/** - tests/modules/nf-core/merquryfk/katcomp/** - merquryfk/katgc: - modules/nf-core/merquryfk/katgc/** - tests/modules/nf-core/merquryfk/katgc/** - merquryfk/merquryfk: - modules/nf-core/merquryfk/merquryfk/** - tests/modules/nf-core/merquryfk/merquryfk/** - merquryfk/ploidyplot: - modules/nf-core/merquryfk/ploidyplot/** - tests/modules/nf-core/merquryfk/ploidyplot/** - meryl/count: - modules/nf-core/meryl/count/** - tests/modules/nf-core/meryl/count/** - meryl/histogram: - modules/nf-core/meryl/histogram/** - tests/modules/nf-core/meryl/histogram/** - meryl/unionsum: - modules/nf-core/meryl/unionsum/** - tests/modules/nf-core/meryl/unionsum/** - metabat2/jgisummarizebamcontigdepths: - modules/nf-core/metabat2/jgisummarizebamcontigdepths/** - tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/** - metabat2/metabat2: - modules/nf-core/metabat2/metabat2/** - tests/modules/nf-core/metabat2/metabat2/** - metaeuk/easypredict: - modules/nf-core/metaeuk/easypredict/** - tests/modules/nf-core/metaeuk/easypredict/** - metaphlan/makedb: - modules/nf-core/metaphlan/makedb/** - tests/modules/nf-core/metaphlan/makedb/** - metaphlan/mergemetaphlantables: - modules/nf-core/metaphlan/mergemetaphlantables/** - tests/modules/nf-core/metaphlan/mergemetaphlantables/** - metaphlan/metaphlan: - modules/nf-core/metaphlan/metaphlan/** - tests/modules/nf-core/metaphlan/metaphlan/** - metaphlan3/mergemetaphlantables: - modules/nf-core/metaphlan3/mergemetaphlantables/** - tests/modules/nf-core/metaphlan3/mergemetaphlantables/** - metaphlan3/metaphlan3: - modules/nf-core/metaphlan3/metaphlan3/** - tests/modules/nf-core/metaphlan3/metaphlan3/** - methyldackel/extract: - modules/nf-core/methyldackel/extract/** - tests/modules/nf-core/methyldackel/extract/** - methyldackel/mbias: - modules/nf-core/methyldackel/mbias/** - tests/modules/nf-core/methyldackel/mbias/** - midas/run: - modules/nf-core/midas/run/** - tests/modules/nf-core/midas/run/** - mindagap/mindagap: - modules/nf-core/mindagap/mindagap/** - tests/modules/nf-core/mindagap/mindagap/** - minia: - modules/nf-core/minia/** - tests/modules/nf-core/minia/** - miniasm: - modules/nf-core/miniasm/** - tests/modules/nf-core/miniasm/** - minimap2/index: - modules/nf-core/minimap2/index/** - tests/modules/nf-core/minimap2/index/** - miniprot/align: - modules/miniprot/align/** - tests/modules/miniprot/align/** - miniprot/index: - modules/nf-core/miniprot/index/** - tests/modules/nf-core/miniprot/index/** - miranda: - modules/nf-core/miranda/** - tests/modules/nf-core/miranda/** - mitohifi/findmitoreference: - modules/nf-core/mitohifi/findmitoreference/** - tests/modules/nf-core/mitohifi/findmitoreference/** - mitohifi/mitohifi: - modules/nf-core/mitohifi/mitohifi/** - tests/modules/nf-core/mitohifi/mitohifi/** - mmseqs/cluster: - modules/nf-core/mmseqs/cluster/** - tests/modules/nf-core/mmseqs/cluster/** - mmseqs/createtsv: - modules/nf-core/mmseqs/createtsv/** - tests/modules/nf-core/mmseqs/createtsv/** - mmseqs/databases: - modules/nf-core/mmseqs/databases/** - tests/modules/nf-core/mmseqs/databases/** - mmseqs/easysearch: - modules/nf-core/mmseqs/easysearch/** - tests/modules/nf-core/mmseqs/easysearch/** - mmseqs/search: - modules/nf-core/mmseqs/search/** - tests/modules/nf-core/mmseqs/search/** - mmseqs/tsv2exprofiledb: - modules/nf-core/mmseqs/tsv2exprofiledb/** - tests/modules/nf-core/mmseqs/tsv2exprofiledb/** - mobsuite/recon: - modules/nf-core/mobsuite/recon/** - tests/modules/nf-core/mobsuite/recon/** - motus/downloaddb: - modules/nf-core/motus/downloaddb/** - tests/modules/nf-core/motus/downloaddb/** - motus/merge: - modules/nf-core/motus/merge/** - tests/modules/nf-core/motus/merge/** - motus/profile: - modules/nf-core/motus/profile/** - tests/modules/nf-core/motus/profile/** - msisensor/msi: - modules/nf-core/msisensor/msi/** - tests/modules/nf-core/msisensor/msi/** - msisensor/scan: - modules/nf-core/msisensor/scan/** - tests/modules/nf-core/msisensor/scan/** - msisensor2/msi: - modules/nf-core/msisensor2/msi/** - tests/modules/nf-core/msisensor2/msi/** - msisensor2/scan: - modules/nf-core/msisensor2/scan/** - tests/modules/nf-core/msisensor2/scan/** - msisensorpro/msisomatic: - modules/nf-core/msisensorpro/msisomatic/** - tests/modules/nf-core/msisensorpro/msisomatic/** - msisensorpro/scan: - modules/nf-core/msisensorpro/scan/** - tests/modules/nf-core/msisensorpro/scan/** - mtnucratio: - modules/nf-core/mtnucratio/** - tests/modules/nf-core/mtnucratio/** - multivcfanalyzer: - modules/nf-core/multivcfanalyzer/** - tests/modules/nf-core/multivcfanalyzer/** - mummer: - modules/nf-core/mummer/** - tests/modules/nf-core/mummer/** - muscle: - modules/nf-core/muscle/** - tests/modules/nf-core/muscle/** - mykrobe/predict: - modules/nf-core/mykrobe/predict/** - tests/modules/nf-core/mykrobe/predict/** - nanocomp: - modules/nf-core/nanocomp/** - tests/modules/nf-core/nanocomp/** - nanolyse: - modules/nf-core/nanolyse/** - tests/modules/nf-core/nanolyse/** - nanomonsv/parse: - modules/nf-core/nanomonsv/parse/** - tests/modules/nf-core/nanomonsv/parse/** - ncbigenomedownload: - modules/nf-core/ncbigenomedownload/** - tests/modules/nf-core/ncbigenomedownload/** - ncbitools/vecscreen: - modules/nf-core/ncbitools/vecscreen/** - tests/modules/nf-core/ncbitools/vecscreen/** - nextclade/datasetget: - modules/nf-core/nextclade/datasetget/** - tests/modules/nf-core/nextclade/datasetget/** - nextclade/run: - modules/nf-core/nextclade/run/** - tests/modules/nf-core/nextclade/run/** - nextgenmap: - modules/nf-core/nextgenmap/** - tests/modules/nf-core/nextgenmap/** - ngmaster: - modules/nf-core/ngmaster/** - tests/modules/nf-core/ngmaster/** - ngmerge: - modules/nf-core/ngmerge/** - tests/modules/nf-core/ngmerge/** - ngsbits/samplegender: - modules/nf-core/ngsbits/samplegender/** - tests/modules/nf-core/ngsbits/samplegender/** - ngscheckmate/fastq: - modules/nf-core/ngscheckmate/fastq/** - tests/modules/nf-core/ngscheckmate/fastq/** - ngscheckmate/ncm: - modules/nf-core/ngscheckmate/ncm/** - tests/modules/nf-core/ngscheckmate/ncm/** - ngscheckmate/patterngenerator: - modules/nf-core/ngscheckmate/patterngenerator/** - tests/modules/nf-core/ngscheckmate/patterngenerator/** - ngscheckmate/vafncm: - modules/nf-core/ngscheckmate/vafncm/** - tests/modules/nf-core/ngscheckmate/vafncm/** - nucmer: - modules/nf-core/nucmer/** - tests/modules/nf-core/nucmer/** - odgi/build: - modules/nf-core/odgi/build/** - tests/modules/nf-core/odgi/build_test/** - odgi/draw: - modules/nf-core/odgi/draw/** - tests/modules/nf-core/odgi/draw/** - odgi/layout: - modules/nf-core/odgi/layout/** - tests/modules/nf-core/odgi/layout/** - odgi/sort: - modules/nf-core/odgi/sort/** - tests/modules/nf-core/odgi/sort/** - odgi/squeeze: - modules/nf-core/odgi/squeeze/** - tests/modules/nf-core/odgi/squeeze/** - odgi/stats: - modules/nf-core/odgi/stats/** - tests/modules/nf-core/odgi/stats/** - odgi/unchop: - modules/nf-core/odgi/unchop/** - tests/modules/nf-core/odgi/unchop/** - odgi/view: - modules/nf-core/odgi/view/** - tests/modules/nf-core/odgi/view/** - odgi/viz: - modules/nf-core/odgi/viz/** - tests/modules/nf-core/odgi/viz/** - oncocnv: - modules/nf-core/oncocnv/** - tests/modules/nf-core/oncocnv/** - openms/decoydatabase: - modules/nf-core/openms/decoydatabase/** - tests/modules/nf-core/openms/decoydatabase/** - openms/idfilter: - modules/nf-core/openms/idfilter/** - tests/modules/nf-core/openms/idfilter/** - openms/idmerger: - modules/nf-core/openms/idmerger/** - tests/modules/nf-core/openms/idmerger/** - openms/peakpickerhires: - modules/nf-core/openms/peakpickerhires/** - tests/modules/nf-core/openms/peakpickerhires/** - optitype: - modules/nf-core/optitype/** - tests/modules/nf-core/optitype/** - paftools/sam2paf: - modules/nf-core/paftools/sam2paf/** - test/modules/nf-core/paftools/sam2paf/** - pairix: - modules/nf-core/pairix/** - tests/modules/nf-core/pairix/** - pairtools/dedup: - modules/nf-core/pairtools/dedup/** - tests/modules/nf-core/pairtools/dedup/** - pairtools/flip: - modules/nf-core/pairtools/flip/** - tests/modules/nf-core/pairtools/flip/** - pairtools/merge: - modules/nf-core/pairtools/merge/** - tests/modules/nf-core/pairtools/merge/** - pairtools/parse: - modules/nf-core/pairtools/parse/** - tests/modules/nf-core/pairtools/parse/** - pairtools/restrict: - modules/nf-core/pairtools/restrict/** - tests/modules/nf-core/pairtools/restrict/** - pairtools/select: - modules/nf-core/pairtools/select/** - tests/modules/nf-core/pairtools/select/** - pairtools/sort: - modules/nf-core/pairtools/sort/** - tests/modules/nf-core/pairtools/sort/** - pairtools/stats: - modules/nf-core/pairtools/stats/** - tests/modules/nf-core/pairtools/stats/** - panaroo/run: - modules/nf-core/panaroo/run/** - tests/modules/nf-core/panaroo/run/** - pangolin: - modules/nf-core/pangolin/** - tests/modules/nf-core/pangolin/** - parabricks/applybqsr: - modules/nf-core/parabricks/applybqsr/** - tests/modules/nf-core/parabricks/applybqsr/** - parabricks/fq2bam: - modules/nf-core/parabricks/fq2bam/** - tests/modules/nf-core/parabricks/fq2bam/** - paraclu: - modules/nf-core/paraclu/** - tests/modules/nf-core/paraclu/** - paragraph/idxdepth: - modules/nf-core/paragraph/idxdepth/** - tests/modules/nf-core/paragraph/idxdepth/** - paragraph/multigrmpy: - modules/nf-core/paragraph/multigrmpy/** - tests/modules/nf-core/paragraph/multigrmpy/** - paragraph/vcf2paragraph: - modules/nf-core/paragraph/vcf2paragraph/** - tests/modules/nf-core/paragraph/vcf2paragraph/** - pasty: - modules/nf-core/pasty/** - tests/modules/nf-core/pasty/** - pbbam/pbmerge: - modules/nf-core/pbbam/pbmerge/** - tests/modules/nf-core/pbbam/pbmerge/** - pbccs: - modules/nf-core/pbccs/** - tests/modules/nf-core/pbccs/** - pbptyper: - modules/nf-core/pbptyper/** - tests/modules/nf-core/pbptyper/** - pear: - modules/nf-core/pear/** - tests/modules/nf-core/pear/** - peddy: - modules/nf-core/peddy/** - tests/modules/nf-core/peddy/** - peka: - modules/nf-core/peka/** - tests/modules/nf-core/peka/** - phantompeakqualtools: - modules/nf-core/phantompeakqualtools/** - tests/modules/nf-core/phantompeakqualtools/** - phispy: - modules/nf-core/phispy/** - tests/modules/nf-core/phispy/** - phyloflash: - modules/nf-core/phyloflash/** - tests/modules/nf-core/phyloflash/** - picard/addorreplacereadgroups: - modules/nf-core/picard/addorreplacereadgroups/** - tests/modules/nf-core/picard/addorreplacereadgroups/** - picard/bedtointervallist: - modules/nf-core/picard/bedtointervallist/** - tests/modules/nf-core/picard/bedtointervallist/** - picard/cleansam: - modules/nf-core/picard/cleansam/** - tests/modules/nf-core/picard/cleansam/** - picard/collecthsmetrics: - modules/nf-core/picard/collecthsmetrics/** - tests/modules/nf-core/picard/collecthsmetrics/** - picard/collectinsertsizemetrics: - modules/nf-core/picard/collectinsertsizemetrics/** - tests/modules/nf-core/picard/collectinsertsizemetrics/** - picard/collectmultiplemetrics: - modules/nf-core/picard/collectmultiplemetrics/** - tests/modules/nf-core/picard/collectmultiplemetrics/** - picard/collectrnaseqmetrics: - modules/nf-core/picard/collectrnaseqmetrics/** - tests/modules/nf-core/picard/collectrnaseqmetrics/** - picard/collectwgsmetrics: - modules/nf-core/picard/collectwgsmetrics/** - tests/modules/nf-core/picard/collectwgsmetrics/** - picard/createsequencedictionary: - modules/nf-core/picard/createsequencedictionary/** - tests/modules/nf-core/picard/createsequencedictionary/** - picard/crosscheckfingerprints: - modules/nf-core/picard/crosscheckfingerprints/** - tests/modules/nf-core/picard/crosscheckfingerprints/** - picard/fastqtosam: - modules/nf-core/picard/fastqtosam/** - tests/modules/nf-core/picard/fastqtosam/** - picard/filtersamreads: - modules/nf-core/picard/filtersamreads/** - tests/modules/nf-core/picard/filtersamreads/** - picard/fixmateinformation: - modules/nf-core/picard/fixmateinformation/** - tests/modules/nf-core/picard/fixmateinformation/** - picard/liftovervcf: - modules/nf-core/picard/liftovervcf/** - tests/modules/nf-core/picard/liftovervcf/** - picard/mergesamfiles: - modules/nf-core/picard/mergesamfiles/** - tests/modules/nf-core/picard/mergesamfiles/** - picard/renamesampleinvcf: - modules/nf-core/picard/renamesampleinvcf/** - tests/modules/nf-core/picard/renamesampleinvcf/** - picard/scatterintervalsbyns: - modules/nf-core/picard/scatterintervalsbyns/** - tests/modules/nf-core/picard/scatterintervalsbyns/** - picard/sortsam: - modules/nf-core/picard/sortsam/** - tests/modules/nf-core/picard/sortsam/** - picard/sortvcf: - modules/nf-core/picard/sortvcf/** - tests/modules/nf-core/picard/sortvcf/** - pilon: - modules/nf-core/pilon/** - tests/modules/nf-core/pilon/** - pindel/pindel: - modules/nf-core/pindel/pindel/** - tests/modules/nf-core/pindel/pindel/** - pints/caller: - modules/nf-core/pints/caller/** - tests/modules/nf-core/pints/caller/** - pirate: - modules/nf-core/pirate/** - tests/modules/nf-core/pirate/** - plasmidfinder: - modules/nf-core/plasmidfinder/** - tests/modules/nf-core/plasmidfinder/** - plasmidid: - modules/nf-core/plasmidid/** - tests/modules/nf-core/plasmidid/** - platypus: - modules/nf-core/platypus/** - tests/modules/nf-core/platypus/** - plink/bcf: - modules/nf-core/plink/bcf/** - tests/modules/nf-core/plink/bcf/** - plink/exclude: - modules/nf-core/plink/exclude/** - tests/modules/nf-core/plink/exclude/** - plink/extract: - modules/nf-core/plink/extract/** - tests/modules/nf-core/plink/extract/** - plink/indep: - modules/nf-core/plink/indep/** - tests/modules/nf-core/plink/indep/** - plink/indeppairwise: - modules/nf-core/plink/indeppairwise/** - tests/modules/nf-core/plink/indeppairwise/** - plink/recode: - modules/nf-core/plink/recode/** - tests/modules/nf-core/plink/recode/** - plink/vcf: - modules/nf-core/plink/vcf/** - tests/modules/nf-core/plink/vcf/** - pmdtools/filter: - modules/nf-core/pmdtools/filter/** - tests/modules/nf-core/pmdtools/filter/** - pneumocat: - modules/nf-core/pneumocat/** - tests/modules/nf-core/pneumocat/** - porechop/abi: - modules/nf-core/porechop/abi/** - tests/modules/nf-core/porechop/abi/** - porechop/porechop: - modules/nf-core/porechop/porechop/** - tests/modules/nf-core/porechop/porechop/** - preseq/ccurve: - modules/nf-core/preseq/ccurve/** - tests/modules/nf-core/preseq/ccurve/** - pretextmap: - modules/nf-core/pretextmap/** - tests/modules/nf-core/pretextmap/** - pretextsnapshot: - modules/nf-core/pretextsnapshot/** - tests/modules/nf-core/pretextsnapshot/** - prinseqplusplus: - modules/nf-core/prinseqplusplus/** - tests/modules/nf-core/prinseqplusplus/** - prodigal: - modules/nf-core/prodigal/** - tests/modules/nf-core/prodigal/** - prokka: - modules/nf-core/prokka/** - tests/modules/nf-core/prokka/** - propr/logratio: - modules/nf-core/propr/logratio/** - tests/modules/nf-core/propr/logratio/** - propr/propd: - modules/nf-core/propr/propd/** - tests/modules/nf-core/propr/propd/** - proteus/readproteingroups: - modules/nf-core/proteus/readproteingroups/** - tests/modules/nf-core/proteus/readproteingroups/** - pureclip: - modules/nf-core/pureclip/** - tests/modules/nf-core/pureclip/** - purecn/coverage: - modules/nf-core/purecn/coverage/** - tests/modules/nf-core/purecn/coverage/** - purecn/intervalfile: - modules/nf-core/purecn/intervalfile/** - tests/modules/nf-core/purecn/intervalfile/** - purecn/normaldb: - modules/nf-core/purecn/normaldb/** - tests/modules/nf-core/purecn/normaldb/** - purecn/run: - modules/nf-core/purecn/run/** - tests/modules/nf-core/purecn/run/** - purgedups/calcuts: - modules/nf-core/purgedups/calcuts/** - tests/modules/nf-core/purgedups/calcuts/** - purgedups/getseqs: - modules/nf-core/purgedups/getseqs/** - tests/modules/nf-core/purgedups/getseqs/** - purgedups/histplot: - modules/nf-core/purgedups/histplot/** - tests/modules/nf-core/purgedups/histplot/** - purgedups/pbcstat: - modules/nf-core/purgedups/pbcstat/** - tests/modules/nf-core/purgedups/pbcstat/** - purgedups/purgedups: - modules/nf-core/purgedups/purgedups/** - tests/modules/nf-core/purgedups/purgedups/** - purgedups/splitfa: - modules/nf-core/purgedups/splitfa/** - tests/modules/nf-core/purgedups/splitfa/** - pydamage/analyze: - modules/nf-core/pydamage/analyze/** - tests/modules/nf-core/pydamage/analyze/** - pydamage/filter: - modules/nf-core/pydamage/filter/** - tests/modules/nf-core/pydamage/filter/** - pyrodigal: - modules/nf-core/pyrodigal/** - tests/modules/nf-core/pyrodigal/** - qcat: - modules/nf-core/qcat/** - tests/modules/nf-core/qcat/** - qualimap/bamqc: - modules/nf-core/qualimap/bamqc/** - tests/modules/nf-core/qualimap/bamqc/** - qualimap/bamqccram: - modules/nf-core/qualimap/bamqccram/** - tests/modules/nf-core/qualimap/bamqccram/** - quast: - modules/nf-core/quast/** - tests/modules/nf-core/quast/** - quilt/quilt: - modules/nf-core/quilt/quilt/** - tests/modules/nf-core/quilt/quilt/** - racon: - modules/nf-core/racon/** - tests/modules/nf-core/racon/** - rapidnj: - modules/nf-core/rapidnj/** - tests/modules/nf-core/rapidnj/** - raven: - modules/nf-core/raven/** - tests/modules/nf-core/raven/** - raxmlng: - modules/nf-core/raxmlng/** - tests/modules/nf-core/raxmlng/** - rgi/main: - modules/nf-core/rgi/main/** - tests/modules/nf-core/rgi/main/** - rhocall/annotate: - modules/nf-core/rhocall/annotate/** - tests/modules/nf-core/rhocall/annotate/** - rmarkdownnotebook: - modules/nf-core/rmarkdownnotebook/** - tests/modules/nf-core/rmarkdownnotebook/** - roary: - modules/nf-core/roary/** - tests/modules/nf-core/roary/** - rtgtools/format: - modules/nf-core/rtgtools/format/** - tests/modules/nf-core/rtgtools/format/** - rtgtools/pedfilter: - modules/nf-core/rtgtools/pedfilter/** - tests/modules/nf-core/rtgtools/pedfilter/** - rtgtools/vcfeval: - modules/nf-core/rtgtools/vcfeval/** - tests/modules/nf-core/rtgtools/vcfeval/** - salsa2: - modules/nf-core/salsa2/** - tests/modules/nf-core/salsa2/** - sam2lca/analyze: - modules/nf-core/sam2lca/analyze/** - tests/modules/nf-core/sam2lca/analyze/** - sambamba/flagstat: - modules/nf-core/sambamba/flagstat/** - tests/modules/nf-core/sambamba/flagstat/** - sambamba/markdup: - modules/nf-core/sambamba/markdup/** - tests/modules/nf-core/sambamba/markdup/** - samblaster: - modules/nf-core/samblaster/** - tests/modules/nf-core/samblaster/** - samtools/collatefastq: - modules/nf-core/samtools/collatefastq/** - tests/modules/nf-core/samtools/collatefastq/** - samtools/coverage: - modules/nf-core/samtools/coverage/** - tests/modules/nf-core/samtools/coverage/** - samtools/depth: - modules/nf-core/samtools/depth/** - tests/modules/nf-core/samtools/depth/** - samtools/dict: - modules/nf-core/samtools/dict/** - tests/modules/nf-core/samtools/dict/** - samtools/faidx: - modules/nf-core/samtools/faidx/** - tests/modules/nf-core/samtools/faidx/** - samtools/fasta: - modules/nf-core/samtools/fasta/** - tests/modules/nf-core/samtools/fasta/** - samtools/getrg: - modules/nf-core/samtools/getrg/** - tests/modules/nf-core/samtools/getrg/** - samtools/import: - modules/nf-core/samtools/import/** - tests/modules/nf-core/samtools/import/** - samtools/markdup: - modules/nf-core/samtools/markdup/** - tests/modules/nf-core/samtools/markdup/** - samtools/reheader: - modules/nf-core/samtools/reheader/** - tests/modules/nf-core/samtools/reheader/** - scimap/mcmicro: - modules/nf-core/scimap/mcmicro/** - tests/modules/nf-core/scimap/mcmicro/** - scoary: - modules/nf-core/scoary/** - tests/modules/nf-core/scoary/** - scramble/clusteranalysis: - modules/nf-core/scramble/clusteranalysis/** - tests/modules/nf-core/scramble/clusteranalysis/** - scramble/clusteridentifier: - modules/nf-core/scramble/clusteridentifier/** - tests/modules/nf-core/scramble/clusteridentifier/** - seacr/callpeak: - modules/nf-core/seacr/callpeak/** - tests/modules/nf-core/seacr/callpeak/** - segemehl/align: - modules/nf-core/segemehl/align/** - tests/modules/nf-core/segemehl/align/** - segemehl/index: - modules/nf-core/segemehl/index/** - tests/modules/nf-core/segemehl/index/** - semibin/singleeasybin: - modules/nf-core/semibin/singleeasybin/** - tests/modules/nf-core/semibin/singleeasybin/** - sentieon/applyvarcal: - modules/nf-core/sentieon/applyvarcal/** - tests/modules/nf-core/sentieon/applyvarcal/** - sentieon/bwaindex: - modules/nf-core/sentieon/bwaindex/** - tests/modules/nf-core/sentieon/bwaindex/** - sentieon/bwamem: - modules/nf-core/sentieon/bwamem/** - tests/modules/nf-core/sentieon/bwamem/** - sentieon/datametrics: - modules/nf-core/sentieon/datametrics/** - tests/modules/nf-core/sentieon/datametrics/** - sentieon/dedup: - modules/nf-core/sentieon/dedup/** - tests/modules/nf-core/sentieon/dedup/** - sentieon/dnamodelapply: - modules/nf-core/sentieon/dnamodelapply/** - tests/modules/nf-core/sentieon/dnamodelapply/** - sentieon/dnascope: - modules/nf-core/sentieon/dnascope/** - tests/modules/nf-core/sentieon/dnascope/** - sentieon/gvcftyper: - modules/nf-core/sentieon/gvcftyper/** - tests/modules/nf-core/sentieon/gvcftyper/** - sentieon/haplotyper: - modules/nf-core/sentieon/haplotyper/** - tests/modules/nf-core/sentieon/haplotyper/** - sentieon/readwriter: - modules/nf-core/sentieon/readwriter/** - tests/modules/nf-core/sentieon/readwriter/** - sentieon/tnfilter: - modules/nf-core/sentieon/tnfilter/** - tests/modules/nf-core/sentieon/tnfilter/** - sentieon/tnhaplotyper2: - modules/nf-core/sentieon/tnhaplotyper2/** - tests/modules/nf-core/sentieon/tnhaplotyper2/** - sentieon/tnscope: - modules/nf-core/sentieon/tnscope/** - tests/modules/nf-core/sentieon/tnscope/** - sentieon/varcal: - modules/nf-core/sentieon/varcal/** - tests/modules/nf-core/sentieon/varcal/** - sentieon/wgsmetrics: - modules/nf-core/sentieon/wgsmetrics/** - tests/modules/nf-core/sentieon/wgsmetrics/** - seqkit/fx2tab: - modules/nf-core/seqkit/fx2tab/** - tests/modules/nf-core/seqkit/fx2tab/** - seqkit/grep: - modules/nf-core/seqkit/grep/** - tests/modules/nf-core/seqkit/grep/** - seqkit/pair: - modules/nf-core/seqkit/pair/** - tests/modules/nf-core/seqkit/pair/** - seqkit/replace: - modules/nf-core/seqkit/replace/** - tests/modules/nf-core/seqkit/replace/** - seqkit/sliding: - modules/nf-core/seqkit/sliding/** - tests/modules/nf-core/seqkit/sliding/** - seqkit/split2: - modules/nf-core/seqkit/split2/** - tests/modules/nf-core/seqkit/split2/** - seqkit/stats: - modules/nf-core/seqkit/stats/** - tests/modules/nf-core/seqkit/stats/** - seqkit/tab2fx: - modules/nf-core/seqkit/tab2fx/** - tests/modules/nf-core/seqkit/tab2fx/** - seqsero2: - modules/nf-core/seqsero2/** - tests/modules/nf-core/seqsero2/** - seqtk/cutn: - modules/nf-core/seqtk/cutn/** - tests/modules/nf-core/seqtk/cutn/** - seqtk/mergepe: - modules/nf-core/seqtk/mergepe/** - tests/modules/nf-core/seqtk/mergepe/** - seqtk/rename: - modules/nf-core/seqtk/rename/** - tests/modules/nf-core/seqtk/rename/** - seqtk/sample: - modules/nf-core/seqtk/sample/** - tests/modules/nf-core/seqtk/sample/** - seqtk/seq: - modules/nf-core/seqtk/seq/** - tests/modules/nf-core/seqtk/seq/** - seqtk/subseq: - modules/nf-core/seqtk/subseq/** - tests/modules/nf-core/seqtk/subseq/** - sequencetools/pileupcaller: - modules/nf-core/sequencetools/pileupcaller/** - tests/modules/nf-core/sequencetools/pileupcaller/** - sequenzautils/bam2seqz: - modules/nf-core/sequenzautils/bam2seqz/** - tests/modules/nf-core/sequenzautils/bam2seqz/** - sequenzautils/gcwiggle: - modules/nf-core/sequenzautils/gcwiggle/** - tests/modules/nf-core/sequenzautils/gcwiggle/** - seqwish/induce: - modules/nf-core/seqwish/induce/** - tests/modules/nf-core/seqwish/induce/** - seroba/run: - modules/nf-core/seroba/run/** - tests/modules/nf-core/seroba/run/** - sexdeterrmine: - modules/nf-core/sexdeterrmine/** - tests/modules/nf-core/sexdeterrmine/** - sgdemux: - modules/nf-core/sgdemux/** - modules/nf-core/untar/** - tests/modules/nf-core/sgdemux/** - shapeit5/ligate: - modules/nf-core/shapeit5/ligate/** - tests/modules/nf-core/shapeit5/ligate/** - shapeit5/phasecommon: - modules/nf-core/shapeit5/phasecommon/** - tests/modules/nf-core/shapeit5/phasecommon/** - shapeit5/phaserare: - modules/nf-core/shapeit5/phaserare/** - tests/modules/nf-core/shapeit5/phaserare/** - shapeit5/switch: - modules/nf-core/shapeit5/switch/** - tests/modules/nf-core/shapeit5/switch/** - shasta: - modules/nf-core/shasta/** - tests/modules/nf-core/shasta/** - shasum: - modules/nf-core/shasum/** - tests/modules/nf-core/shasum/** - shigatyper: - modules/nf-core/shigatyper/** - tests/modules/nf-core/shigatyper/** - shigeifinder: - modules/nf-core/shigeifinder/** - tests/modules/nf-core/shigeifinder/** - shinyngs/app: - modules/nf-core/shinyngs/app/** - tests/modules/nf-core/shinyngs/app/** - shinyngs/staticdifferential: - modules/nf-core/shinyngs/staticdifferential/** - tests/modules/nf-core/shinyngs/staticdifferential/** - shinyngs/staticexploratory: - modules/nf-core/shinyngs/staticexploratory/** - tests/modules/nf-core/shinyngs/staticexploratory/** - shinyngs/validatefomcomponents: - modules/nf-core/shinyngs/validatefomcomponents/** - tests/modules/nf-core/shinyngs/validatefomcomponents/** - shovill: - modules/nf-core/shovill/** - tests/modules/nf-core/shovill/** - sickle: - modules/nf-core/sickle/** - tests/modules/nf-core/sickle/** - simpleaf/index: - modules/nf-core/simpleaf/index/** - tests/modules/nf-core/simpleaf/index/** - simpleaf/quant: - modules/nf-core/simpleaf/quant/** - tests/modules/nf-core/simpleaf/quant/** - sistr: - modules/nf-core/sistr/** - tests/modules/nf-core/sistr/** - slimfastq: - modules/nf-core/slimfastq/** - tests/modules/nf-core/slimfastq/** - smncopynumbercaller: - modules/nf-core/smncopynumbercaller/** - tests/modules/nf-core/smncopynumbercaller/** - smoothxg: - modules/nf-core/smoothxg/** - tests/modules/nf-core/smoothxg/** - smoove/call: - modules/nf-core/smoove/call/** - tests/modules/nf-core/smoove/call/** - snapaligner/align: - modules/nf-core/snapaligner/align/** - tests/modules/nf-core/snapaligner/align/** - snapaligner/index: - modules/nf-core/snapaligner/index/** - tests/modules/nf-core/snapaligner/index/** - sniffles: - modules/nf-core/sniffles/** - tests/modules/nf-core/sniffles/** - snippy/core: - modules/nf-core/snippy/core/** - tests/modules/nf-core/snippy/core/** - snippy/run: - modules/nf-core/snippy/run/** - tests/modules/nf-core/snippy/run/** - snpdists: - modules/nf-core/snpdists/** - tests/modules/nf-core/snpdists/** - snpeff/download: - modules/nf-core/snpeff/download/** - tests/modules/nf-core/snpeff/download/** - snpeff/snpeff: - modules/nf-core/snpeff/snpeff/** - tests/modules/nf-core/snpeff/snpeff/** - snpsift/annotate: - modules/nf-core/snpsift/annotate/** - tests/modules/nf-core/snpsift/annotate/** - snpsift/dbnsfp: - modules/nf-core/snpsift/dbnsfp/** - tests/modules/nf-core/snpsift/dbnsfp/** - snpsift/split: - modules/nf-core/snpsift/split/** - tests/modules/nf-core/snpsift/split/** - snpsites: - modules/nf-core/snpsites/** - tests/modules/nf-core/snpsites/** - somalier/ancestry: - modules/nf-core/somalier/ancestry/** - tests/modules/nf-core/somalier/ancestry/** - somalier/extract: - modules/nf-core/somalier/extract/** - tests/modules/nf-core/somalier/extract/** - somalier/relate: - modules/nf-core/somalier/relate/** - tests/modules/nf-core/somalier/relate/** - sourmash/compare: - modules/nf-core/sourmash/compare/** - tests/modules/nf-core/sourmash/compare/** - sourmash/gather: - modules/nf-core/sourmash/gather/** - tests/modules/nf-core/sourmash/gather/** - sourmash/index: - modules/nf-core/sourmash/index/** - tests/modules/nf-core/sourmash/index/** - sourmash/taxannotate: - modules/nf-core/sourmash/taxannotate/** - tests/modules/nf-core/sourmash/taxannotate/** - spaceranger/count: - modules/nf-core/spaceranger/count/** - tests/modules/nf-core/spaceranger/count/** - spaceranger/mkgtf: - modules/nf-core/spaceranger/mkgtf/** - tests/modules/nf-core/spaceranger/mkgtf/** - spaceranger/mkref: - modules/nf-core/spaceranger/mkref/** - tests/modules/nf-core/spaceranger/mkref/** - spades: - modules/nf-core/spades/** - tests/modules/nf-core/spades/** - spatyper: - modules/nf-core/spatyper/** - tests/modules/nf-core/spatyper/** - spring/compress: - modules/nf-core/spring/compress/** - tests/modules/nf-core/spring/compress/** - spring/decompress: - modules/nf-core/spring/decompress/** - tests/modules/nf-core/spring/decompress/** - srst2/srst2: - modules/nf-core/srst2/srst2/** - tests/modules/nf-core/srst2/srst2/** - ssuissero: - modules/nf-core/ssuissero/** - tests/modules/nf-core/ssuissero/** - stadeniolib/scramble: - modules/nf-core/stadeniolib/scramble/** - tests/modules/nf-core/stadeniolib/scramble/** - staphopiasccmec: - modules/nf-core/staphopiasccmec/** - tests/modules/nf-core/staphopiasccmec/** - star/starsolo: - modules/nf-core/star/starsolo/** - tests/modules/nf-core/star/starsolo/** - stecfinder: - modules/nf-core/stecfinder/** - tests/modules/nf-core/stecfinder/** - stitch: - modules/nf-core/stitch/** - tests/modules/nf-core/stitch/** - stranger: - modules/nf-core/stranger/** - tests/modules/nf-core/stranger/** - strelka/germline: - modules/nf-core/strelka/germline/** - tests/modules/nf-core/strelka/germline/** - strelka/somatic: - modules/nf-core/strelka/somatic/** - tests/modules/nf-core/strelka/somatic/** - subworkflows/align_bowtie2: - subworkflows/nf-core/align_bowtie2/** - tests/subworkflows/nf-core/align_bowtie2/** - subworkflows/bam_cnv_wisecondorx: - subworkflows/nf-core/bam_cnv_wisecondorx/** - tests/subworkflows/nf-core/bam_cnv_wisecondorx/** - subworkflows/bam_create_som_pon_gatk: - subworkflows/nf-core/bam_create_som_pon_gatk/** - tests/subworkflows/nf-core/bam_create_som_pon_gatk/** - subworkflows/bam_docounts_contamination_angsd: - subworkflows/nf-core/bam_docounts_contamination_angsd/** - tests/subworkflows/nf-core/bam_docounts_contamination_angsd/** - subworkflows/bam_markduplicates_picard: - subworkflows/nf-core/bam_markduplicates_picard/** - tests/subworkflows/nf-core/bam_markduplicates_picard/** - subworkflows/bam_markduplicates_samtools: - subworkflows/nf-core/bam_markduplicates_samtools/** - tests/subworkflows/nf-core/bam_markduplicates_samtools/** - subworkflows/bam_ngscheckmate: - subworkflows/nf-core/bam_ngscheckmate/** - tests/subworkflows/nf-core/bam_ngscheckmate/** - subworkflows/bam_qc_picard: - subworkflows/nf-core/bam_qc_picard/** - tests/subworkflows/nf-core/bam_qc_picard/** - subworkflows/bam_sort_samtools: - subworkflows/nf-core/bam_sort_samtools/** - tests/subworkflows/nf-core/bam_sort_samtools/** - subworkflows/bam_split_by_region: - subworkflows/nf-core/bam_split_by_region/** - tests/subworkflows/nf-core/bam_split_by_region/** - subworkflows/bam_tumor_normal_somatic_variant_calling_gatk: - subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/** - tests/subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/** - subworkflows/bam_tumor_only_somatic_variant_calling_gatk: - subworkflows/nf-core/bam_tumor_only_somatic_variant_calling_gatk/** - tests/subworkflows/nf-core/bam_tumor_only_somatic_variant_calling_gatk/** - subworkflows/bam_variant_calling_sort_freebayes_bcftools: - subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/** - tests/subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/** - subworkflows/bam_variant_demix_boot_freyja: - subworkflows/nf-core/bam_variant_demix_boot_freyja/** - tests/subworkflows/nf-core/bam_variant_demix_boot_freyja/** - subworkflows/bcl_demultiplex: - subworkflows/nf-core/bcl_demultiplex/** - tests/subworkflows/nf-core/bcl_demultiplex/** - subworkflows/bed_scatter_bedtools: - subworkflows/nf-core/bed_scatter_bedtools/** - tests/subworkflows/nf-core/bed_scatter_bedtools/** - subworkflows/fasta_binning_concoct: - subworkflows/nf-core/fasta_binning_concoct/** - tests/subworkflows/nf-core/fasta_binning_concoct/** - subworkflows/fasta_clean_fcs: - subworkflows/nf-core/fasta_clean_fcs/** - tests/subworkflows/nf-core/fasta_clean_fcs/** - subworkflows/fasta_index_dna: - subworkflows/nf-core/fasta_index_dna/** - tests/subworkflows/nf-core/fasta_index_dna/** - subworkflows/fasta_newick_epang_gappa: - subworkflows/nf-core/fasta_newick_epang_gappa/** - tests/subworkflows/nf-core/fasta_newick_epang_gappa/** - subworkflows/fastq_align_bamcmp_bwa: - subworkflows/nf-core/fastq_align_bamcmp_bwa/** - tests/subworkflows/nf-core/fastq_align_bamcmp_bwa/** - subworkflows/fastq_align_bowtie2: - subworkflows/nf-core/fastq_align_bowtie2/** - tests/subworkflows/nf-core/fastq_align_bowtie2/** - subworkflows/fastq_align_bwa: - subworkflows/nf-core/fastq_align_bwa/** - tests/subworkflows/nf-core/fastq_align_bwa/** - subworkflows/fastq_align_bwaaln: - subworkflows/nf-core/fastq_align_bwaaln/** - tests/subworkflows/nf-core/fastq_align_bwaaln/** - subworkflows/fastq_align_chromap: - subworkflows/nf-core/fastq_align_chromap/** - tests/subworkflows/nf-core/fastq_align_chromap/** - subworkflows/fastq_align_dna: - subworkflows/nf-core/fastq_align_dna/** - tests/subworkflows/nf-core/fastq_align_dna/** - subworkflows/fastq_align_hisat2: - subworkflows/nf-core/fastq_align_hisat2/** - tests/subworkflows/nf-core/fastq_align_hisat2/** - subworkflows/fastq_align_star: - subworkflows/nf-core/fastq_align_star/** - tests/subworkflows/nf-core/fastq_align_star/** - subworkflows/fastq_contam_seqtk_kraken: - subworkflows/nf-core/fastq_contam_seqtk_kraken/** - tests/subworkflows/nf-core/fastq_contam_seqtk_kraken/** - subworkflows/fastq_create_umi_consensus_fgbio: - subworkflows/nf-core/fastq_create_umi_consensus_fgbio/** - tests/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/** - subworkflows/fastq_fastqc_umitools_trimgalore: - subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/** - tests/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/** - subworkflows/fastq_trim_fastp_fastqc: - subworkflows/nf-core/fastq_trim_fastp_fastqc/** - tests/subworkflows/nf-core/fastq_trim_fastp_fastqc/** - subworkflows/gatk_create_som_pon: - subworkflows/nf-core/gatk_create_som_pon/** - tests/subworkflows/nf-core/gatk_create_som_pon/** - subworkflows/homer/groseq: - subworkflows/nf-core/homer/groseq/** - tests/subworkflows/nf-core/homer/groseq/** - subworkflows/initialise: - subworkflows/nf-core/initialise/** - tests/subworkflows/nf-core/initialise/** - subworkflows/multiple_impute_glimpse2: - subworkflows/nf-core/multiple_impute_glimpse2/** - tests/subworkflows/nf-core/multiple_impute_glimpse2/** - subworkflows/utils_nextflow_pipeline: - subworkflows/nf-core/utils_nextflow_pipeline/** - tests/subworkflows/nf-core/utils_nextflow_pipeline/** - subworkflows/utils_nfcore_pipeline: - subworkflows/nf-core/utils_nfcore_pipeline/** - tests/subworkflows/nf-core/utils_nfcore_pipeline/** - subworkflows/vcf_annotate_ensemblvep: - subworkflows/nf-core/vcf_annotate_ensemblvep/** - tests/subworkflows/nf-core/vcf_annotate_ensemblvep/** - subworkflows/vcf_annotate_ensemblvep_snpeff: - subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/** - tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/** - subworkflows/vcf_annotate_snpeff: - subworkflows/nf-core/vcf_annotate_snpeff/** - tests/subworkflows/nf-core/vcf_annotate_snpeff/** - subworkflows/vcf_extract_relate_somalier: - subworkflows/nf-core/vcf_extract_relate_somalier/** - tests/subworkflows/nf-core/vcf_extract_relate_somalier/** - subworkflows/vcf_gather_bcftools: - subworkflows/nf-core/vcf_gather_bcftools/** - tests/subworkflows/nf-core/vcf_gather_bcftools/** - subworkflows/vcf_phase_shapeit5: - subworkflows/nf-core/vcf_phase_shapeit5/** - tests/subworkflows/nf-core/vcf_phase_shapeit5/** - survivor/filter: - modules/nf-core/survivor/filter/** - tests/modules/nf-core/survivor/filter/** - survivor/merge: - modules/nf-core/survivor/merge/** - tests/modules/nf-core/survivor/merge/** - survivor/simsv: - modules/nf-core/survivor/simsv/** - tests/modules/nf-core/survivor/simsv/** - svaba: - modules/nf-core/svaba/** - tests/modules/nf-core/svaba/** - svdb/merge: - modules/nf-core/svdb/merge/** - tests/modules/nf-core/svdb/merge/** - svtk/baftest: - modules/nf-core/svtk/baftest/** - tests/modules/nf-core/svtk/baftest/** - svtk/countsvtypes: - modules/nf-core/svtk/countsvtypes/** - tests/modules/nf-core/svtk/countsvtypes/** - svtk/rdtest2vcf: - modules/nf-core/svtk/rdtest2vcf/** - tests/modules/nf-core/svtk/rdtest2vcf/** - svtk/standardize: - modules/nf-core/svtk/standardize/** - tests/modules/nf-core/svtk/standardize/** - svtk/vcf2bed: - modules/nf-core/svtk/vcf2bed/** - tests/modules/nf-core/svtk/vcf2bed/** - svtyper/svtyper: - modules/nf-core/svtyper/svtyper/** - tests/modules/nf-core/svtyper/svtyper/** - tabix/bgzip: - modules/nf-core/tabix/bgzip/** - tests/modules/nf-core/tabix/bgzip/** - tabix/bgziptabix: - modules/nf-core/tabix/bgziptabix/** - tests/modules/nf-core/tabix/bgziptabix/** - tabix/tabix: - modules/nf-core/tabix/tabix/** - tests/modules/nf-core/tabix/tabix/** - tailfindr: - modules/nf-core/tailfindr/** - tests/modules/nf-core/tailfindr/** - taxpasta/merge: - modules/nf-core/taxpasta/merge/** - tests/modules/nf-core/taxpasta/merge/** - taxpasta/standardise: - modules/nf-core/taxpasta/standardise/** - tests/modules/nf-core/taxpasta/standardise/** - tbprofiler/profile: - modules/nf-core/tbprofiler/profile/** - tests/modules/nf-core/tbprofiler/profile/** - tiara/tiara: - modules/nf-core/tiara/tiara/** - tests/modules/nf-core/tiara/tiara/** - tiddit/cov: - modules/nf-core/tiddit/cov/** - tests/modules/nf-core/tiddit/cov/** - tiddit/sv: - modules/nf-core/tiddit/sv/** - tests/modules/nf-core/tiddit/sv/** - topas/gencons: - modules/nf-core/topas/gencons/** - tests/modules/nf-core/topas/gencons/** - transdecoder/longorf: - modules/nf-core/transdecoder/longorf/** - tests/modules/nf-core/transdecoder/longorf/** - transdecoder/predict: - modules/nf-core/transdecoder/predict/** - tests/modules/nf-core/transdecoder/predict/** - trinity: - modules/nf-core/trinity/** - tests/modules/nf-core/trinity/** - truvari/bench: - modules/nf-core/truvari/bench/** - tests/modules/nf-core/truvari/bench/** - ucsc/bedtobigbed: - modules/nf-core/ucsc/bedtobigbed/** - tests/modules/nf-core/ucsc/bedtobigbed/** - ucsc/bigwigaverageoverbed: - modules/nf-core/ucsc/bigwigaverageoverbed/** - tests/modules/nf-core/ucsc/bigwigaverageoverbed/** - ucsc/gtftogenepred: - modules/nf-core/ucsc/gtftogenepred/** - tests/modules/nf-core/ucsc/gtftogenepred/** - ucsc/liftover: - modules/nf-core/ucsc/liftover/** - tests/modules/nf-core/ucsc/liftover/** - ucsc/wigtobigwig: - modules/nf-core/ucsc/wigtobigwig/** - tests/modules/nf-core/ucsc/wigtobigwig/** - ultra/align: - modules/nf-core/ultra/align/** - tests/modules/nf-core/ultra/align/** - ultra/index: - modules/nf-core/ultra/index/** - tests/modules/nf-core/ultra/index/** - ultra/pipeline: - modules/nf-core/ultra/pipeline/** - tests/modules/nf-core/ultra/pipeline/** - ultraplex: - modules/nf-core/ultraplex/** - tests/modules/nf-core/ultraplex/** - umicollapse: - modules/nf-core/umicollapse/** - tests/modules/nf-core/umicollapse/** - umitools/dedup: - modules/nf-core/umitools/dedup/** - tests/modules/nf-core/umitools/dedup/** - umitools/group: - modules/nf-core/umitools/group/** - tests/modules/nf-core/umitools/group/** - unicycler: - modules/nf-core/unicycler/** - tests/modules/nf-core/unicycler/** - universc: - modules/nf-core/universc/** - tests/modules/nf-core/universc/** - untarfiles: - modules/nf-core/untarfiles/** - tests/modules/nf-core/untarfiles/** - unzip: - modules/nf-core/unzip/** - tests/modules/nf-core/unzip/** - unzipfiles: - modules/nf-core/unzipfiles/** - tests/modules/nf-core/unzipfiles/** - upd: - modules/nf-core/upd/** - tests/modules/nf-core/upd/** - variantbam: - modules/nf-core/variantbam/** - tests/modules/nf-core/variantbam/** - varlociraptor/callvariants: - modules/nf-core/varlociraptor/callvariants/** - tests/modules/nf-core/varlociraptor/callvariants/** - varlociraptor/estimatealignmentproperties: - modules/nf-core/varlociraptor/estimatealignmentproperties/** - tests/modules/nf-core/varlociraptor/estimatealignmentproperties/** - varlociraptor/preprocess: - modules/nf-core/varlociraptor/preprocess/** - tests/modules/nf-core/varlociraptor/preprocess/** - vcf2cytosure: - modules/nf-core/vcf2cytosure/** - tests/modules/nf-core/vcf2cytosure/** - vcf2db: - modules/nf-core/vcf2db/** - tests/modules/nf-core/vcf2db/** - vcf2maf: - modules/nf-core/vcf2maf/** - tests/modules/nf-core/vcf2maf/** - vcfanno: - modules/nf-core/vcfanno/** - tests/modules/nf-core/vcfanno/** - vcflib/vcfbreakmulti: - modules/nf-core/vcflib/vcfbreakmulti/** - tests/modules/nf-core/vcflib/vcfbreakmulti/** - vcflib/vcffilter: - modules/nf-core/vcflib/vcffilter/** - tests/modules/nf-core/vcflib/vcffilter/** - vcflib/vcfuniq: - modules/nf-core/vcflib/vcfuniq/** - tests/modules/nf-core/vcflib/vcfuniq/** - vcftools: - modules/nf-core/vcftools/** - tests/modules/nf-core/vcftools/** - verifybamid/verifybamid: - modules/nf-core/verifybamid/verifybamid/** - tests/modules/nf-core/verifybamid/verifybamid/** - verifybamid/verifybamid2: - modules/nf-core/verifybamid/verifybamid2/** - tests/modules/nf-core/verifybamid/verifybamid2/** - vg/construct: - modules/nf-core/vg/construct/** - tests/modules/nf-core/vg/construct/** - vg/deconstruct: - modules/nf-core/vg/deconstruct/** - tests/modules/nf-core/vg/deconstruct/** - vg/index: - modules/nf-core/vg/index/** - tests/modules/nf-core/vg/index/** - vrhyme/extractunbinned: - modules/nf-core/vrhyme/extractunbinned/** - tests/modules/nf-core/vrhyme/extractunbinned/** - vrhyme/linkbins: - modules/nf-core/vrhyme/linkbins/** - tests/modules/nf-core/vrhyme/linkbins/** - vrhyme/vrhyme: - modules/nf-core/vrhyme/vrhyme/** - tests/modules/nf-core/vrhyme/vrhyme/** - vsearch/cluster: - modules/nf-core/vsearch/cluster/** - tests/modules/nf-core/vsearch/cluster/** - vsearch/sintax: - modules/nf-core/vsearch/sintax/** - tests/modules/nf-core/vsearch/sintax/** - vsearch/sort: - modules/nf-core/vsearch/sort/** - tests/modules/nf-core/vsearch/sort/** - vsearch/usearchglobal: - modules/nf-core/vsearch/usearchglobal/** - tests/modules/nf-core/vsearch/usearchglobal/** - vt/decompose: - modules/nf-core/vt/decompose/** - tests/modules/nf-core/vt/decompose/** - vt/normalize: - modules/nf-core/vt/normalize/** - tests/modules/nf-core/vt/normalize/** - wfmash: - modules/nf-core/wfmash/** - tests/modules/nf-core/wfmash/** - wgsim: - modules/nf-core/wgsim/** - tests/modules/nf-core/wgsim/** - whamg: - modules/nf-core/whamg/** - tests/modules/nf-core/whamg/** - windowmasker/convert: - modules/nf-core/windowmasker/convert/** - tests/modules/nf-core/windowmasker/convert/** - windowmasker/mkcounts: - modules/nf-core/windowmasker/mkcounts/** - tests/modules/windowmasker/mkcounts/** - windowmasker/ustat: - modules/nf-core/windowmasker/ustat/** - tests/modules/windowmasker/ustat/** - wisecondorx/convert: - modules/nf-core/wisecondorx/convert/** - tests/modules/nf-core/wisecondorx/convert/** - wisecondorx/newref: - modules/nf-core/wisecondorx/newref/** - tests/modules/nf-core/wisecondorx/newref/** - wisecondorx/predict: - modules/nf-core/wisecondorx/predict/** - tests/modules/nf-core/wisecondorx/predict/** - yahs: - modules/nf-core/yahs/** - tests/modules/nf-core/yahs/** - yara/index: - modules/nf-core/yara/index/** - tests/modules/nf-core/yara/index/** - yara/mapper: - modules/nf-core/yara/mapper/** - tests/modules/nf-core/yara/mapper/** - zip: - modules/nf-core/zip/** - tests/modules/nf-core/zip/** diff --git a/tests/modules/nf-core/chewbbaca/createschema/main.nf b/tests/modules/nf-core/chewbbaca/createschema/main.nf deleted file mode 100644 index c21fe3c37d8..00000000000 --- a/tests/modules/nf-core/chewbbaca/createschema/main.nf +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { CHEWBBACA_CREATESCHEMA } from '../../../../../modules/nf-core/chewbbaca/createschema/main.nf' - -workflow test_chewbbaca_createschema { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)] - ptf = [] - cds = [] - - CHEWBBACA_CREATESCHEMA ( input, ptf, cds) -} - -workflow test_chewbbaca_createschema_multi { - - input = [ - [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] ] - ptf = [] - cds = [] - - CHEWBBACA_CREATESCHEMA ( input, ptf, cds) -} - -workflow test_chewbbaca_createschema_gz { - - input = [ - [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true)] ] - ptf = [] - cds = [] - - CHEWBBACA_CREATESCHEMA ( input, ptf, cds) -} diff --git a/tests/modules/nf-core/chewbbaca/createschema/test.yml b/tests/modules/nf-core/chewbbaca/createschema/test.yml deleted file mode 100644 index 6e08a1d073e..00000000000 --- a/tests/modules/nf-core/chewbbaca/createschema/test.yml +++ /dev/null @@ -1,234 +0,0 @@ -- name: chewbbaca createschema test_chewbbaca_createschema - command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema -c ./tests/config/nextflow.config - tags: - - chewbbaca - - chewbbaca/createschema - files: - - path: output/chewbbaca/results/cds_coordinates.tsv - md5sum: 7fef49207aa024b68f465e986f4c7444 - - path: output/chewbbaca/results/invalid_cds.txt - md5sum: d0afbd9996054d8838e62dc3e852fa07 - - path: output/chewbbaca/results/test/.genes_list - contains: - - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ' - - path: output/chewbbaca/results/test/.schema_config - md5sum: 92b512f65fde7dce321ada54e5c431e9 - - path: output/chewbbaca/results/test/contigs-protein1.fasta - md5sum: 79f1e1c7105c0b34195e18c34960d2d4 - - path: output/chewbbaca/results/test/contigs-protein10.fasta - md5sum: 9fd40f7247cb3ed93f66828dbbfbac22 - - path: output/chewbbaca/results/test/contigs-protein11.fasta - md5sum: b2f94d1babce56f5c1e46ccd35d2a7d7 - - path: output/chewbbaca/results/test/contigs-protein13.fasta - md5sum: 7314303d55a8598b229eca32ddeea14d - - path: output/chewbbaca/results/test/contigs-protein14.fasta - md5sum: 2a8023e86fb119834f2d050daee33958 - - path: output/chewbbaca/results/test/contigs-protein16.fasta - md5sum: e006bb0da17f845c1672caed826d4ab7 - - path: output/chewbbaca/results/test/contigs-protein17.fasta - md5sum: 58f2501c0a7e48aaa86a87d01740b5c4 - - path: output/chewbbaca/results/test/contigs-protein18.fasta - md5sum: 6b4f385dc954df1fd2057a1c57872338 - - path: output/chewbbaca/results/test/contigs-protein19.fasta - md5sum: 3614c079d0b08f0c59bdaac9dcea0409 - - path: output/chewbbaca/results/test/contigs-protein2.fasta - md5sum: 0b982a66a0f001f11a86cc1b5a4ef80d - - path: output/chewbbaca/results/test/contigs-protein20.fasta - md5sum: 75b2492e5db0848079faafe6f60fe9fd - - path: output/chewbbaca/results/test/contigs-protein4.fasta - md5sum: 4ce5090bf2547bc588f0f8d00ae4a59d - - path: output/chewbbaca/results/test/contigs-protein6.fasta - md5sum: ffebf19b61285767a14f486af7181c30 - - path: output/chewbbaca/results/test/contigs-protein7.fasta - md5sum: ee06d9303c5b7844b003daa42b7a1869 - - path: output/chewbbaca/results/test/contigs-protein8.fasta - md5sum: 2a00efc36b036ab7f6c30f85533963cf - - path: output/chewbbaca/results/test/contigs-protein9.fasta - md5sum: ad9372b812030db327fa12d1e1731e85 - - path: output/chewbbaca/results/test/short/contigs-protein10_short.fasta - md5sum: 9fd40f7247cb3ed93f66828dbbfbac22 - - path: output/chewbbaca/results/test/short/contigs-protein11_short.fasta - md5sum: b2f94d1babce56f5c1e46ccd35d2a7d7 - - path: output/chewbbaca/results/test/short/contigs-protein13_short.fasta - md5sum: 7314303d55a8598b229eca32ddeea14d - - path: output/chewbbaca/results/test/short/contigs-protein14_short.fasta - md5sum: 2a8023e86fb119834f2d050daee33958 - - path: output/chewbbaca/results/test/short/contigs-protein16_short.fasta - md5sum: e006bb0da17f845c1672caed826d4ab7 - - path: output/chewbbaca/results/test/short/contigs-protein17_short.fasta - md5sum: 58f2501c0a7e48aaa86a87d01740b5c4 - - path: output/chewbbaca/results/test/short/contigs-protein18_short.fasta - md5sum: 6b4f385dc954df1fd2057a1c57872338 - - path: output/chewbbaca/results/test/short/contigs-protein19_short.fasta - md5sum: 3614c079d0b08f0c59bdaac9dcea0409 - - path: output/chewbbaca/results/test/short/contigs-protein1_short.fasta - md5sum: 79f1e1c7105c0b34195e18c34960d2d4 - - path: output/chewbbaca/results/test/short/contigs-protein20_short.fasta - md5sum: 75b2492e5db0848079faafe6f60fe9fd - - path: output/chewbbaca/results/test/short/contigs-protein2_short.fasta - md5sum: 0b982a66a0f001f11a86cc1b5a4ef80d - - path: output/chewbbaca/results/test/short/contigs-protein4_short.fasta - md5sum: 4ce5090bf2547bc588f0f8d00ae4a59d - - path: output/chewbbaca/results/test/short/contigs-protein6_short.fasta - md5sum: ffebf19b61285767a14f486af7181c30 - - path: output/chewbbaca/results/test/short/contigs-protein7_short.fasta - md5sum: ee06d9303c5b7844b003daa42b7a1869 - - path: output/chewbbaca/results/test/short/contigs-protein8_short.fasta - md5sum: 2a00efc36b036ab7f6c30f85533963cf - - path: output/chewbbaca/results/test/short/contigs-protein9_short.fasta - md5sum: ad9372b812030db327fa12d1e1731e85 - - path: output/chewbbaca/versions.yml - -- name: chewbbaca createschema test_chewbbaca_createschema_multi - command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema_multi -c ./tests/config/nextflow.config - tags: - - chewbbaca - - chewbbaca/createschema - files: - - path: output/chewbbaca/results/cds_coordinates.tsv - md5sum: e62f4e808939f97ccdbe4d17c1521b6c - - path: output/chewbbaca/results/invalid_cds.txt - md5sum: d0afbd9996054d8838e62dc3e852fa07 - - path: output/chewbbaca/results/test/.genes_list - contains: - - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ' - - path: output/chewbbaca/results/test/.schema_config - md5sum: 92b512f65fde7dce321ada54e5c431e9 - - path: output/chewbbaca/results/test/contigs-protein1.fasta - md5sum: 79f1e1c7105c0b34195e18c34960d2d4 - - path: output/chewbbaca/results/test/contigs-protein10.fasta - md5sum: 9fd40f7247cb3ed93f66828dbbfbac22 - - path: output/chewbbaca/results/test/contigs-protein14.fasta - md5sum: 2a8023e86fb119834f2d050daee33958 - - path: output/chewbbaca/results/test/contigs-protein16.fasta - md5sum: e006bb0da17f845c1672caed826d4ab7 - - path: output/chewbbaca/results/test/contigs-protein17.fasta - md5sum: 58f2501c0a7e48aaa86a87d01740b5c4 - - path: output/chewbbaca/results/test/contigs-protein18.fasta - md5sum: 6b4f385dc954df1fd2057a1c57872338 - - path: output/chewbbaca/results/test/contigs-protein19.fasta - md5sum: 3614c079d0b08f0c59bdaac9dcea0409 - - path: output/chewbbaca/results/test/contigs-protein2.fasta - md5sum: 0b982a66a0f001f11a86cc1b5a4ef80d - - path: output/chewbbaca/results/test/contigs-protein20.fasta - md5sum: 75b2492e5db0848079faafe6f60fe9fd - - path: output/chewbbaca/results/test/contigs-protein4.fasta - md5sum: 4ce5090bf2547bc588f0f8d00ae4a59d - - path: output/chewbbaca/results/test/contigs-protein6.fasta - md5sum: ffebf19b61285767a14f486af7181c30 - - path: output/chewbbaca/results/test/contigs-protein7.fasta - md5sum: ee06d9303c5b7844b003daa42b7a1869 - - path: output/chewbbaca/results/test/contigs-protein8.fasta - md5sum: 2a00efc36b036ab7f6c30f85533963cf - - path: output/chewbbaca/results/test/contigs-protein9.fasta - md5sum: ad9372b812030db327fa12d1e1731e85 - - path: output/chewbbaca/results/test/genome-protein1.fasta - md5sum: c1b28842a7e89e3bcc7d655afe51c609 - - path: output/chewbbaca/results/test/short/contigs-protein10_short.fasta - md5sum: 9fd40f7247cb3ed93f66828dbbfbac22 - - path: output/chewbbaca/results/test/short/contigs-protein14_short.fasta - md5sum: 2a8023e86fb119834f2d050daee33958 - - path: output/chewbbaca/results/test/short/contigs-protein16_short.fasta - md5sum: e006bb0da17f845c1672caed826d4ab7 - - path: output/chewbbaca/results/test/short/contigs-protein17_short.fasta - md5sum: 58f2501c0a7e48aaa86a87d01740b5c4 - - path: output/chewbbaca/results/test/short/contigs-protein18_short.fasta - md5sum: 6b4f385dc954df1fd2057a1c57872338 - - path: output/chewbbaca/results/test/short/contigs-protein19_short.fasta - md5sum: 3614c079d0b08f0c59bdaac9dcea0409 - - path: output/chewbbaca/results/test/short/contigs-protein1_short.fasta - md5sum: 79f1e1c7105c0b34195e18c34960d2d4 - - path: output/chewbbaca/results/test/short/contigs-protein20_short.fasta - md5sum: 75b2492e5db0848079faafe6f60fe9fd - - path: output/chewbbaca/results/test/short/contigs-protein2_short.fasta - md5sum: 0b982a66a0f001f11a86cc1b5a4ef80d - - path: output/chewbbaca/results/test/short/contigs-protein4_short.fasta - md5sum: 4ce5090bf2547bc588f0f8d00ae4a59d - - path: output/chewbbaca/results/test/short/contigs-protein6_short.fasta - md5sum: ffebf19b61285767a14f486af7181c30 - - path: output/chewbbaca/results/test/short/contigs-protein7_short.fasta - md5sum: ee06d9303c5b7844b003daa42b7a1869 - - path: output/chewbbaca/results/test/short/contigs-protein8_short.fasta - md5sum: 2a00efc36b036ab7f6c30f85533963cf - - path: output/chewbbaca/results/test/short/contigs-protein9_short.fasta - md5sum: ad9372b812030db327fa12d1e1731e85 - - path: output/chewbbaca/results/test/short/genome-protein1_short.fasta - md5sum: c1b28842a7e89e3bcc7d655afe51c609 - - path: output/chewbbaca/versions.yml - -- name: chewbbaca createschema test_chewbbaca_createschema_gz - command: nextflow run ./tests/modules/nf-core/chewbbaca/createschema -entry test_chewbbaca_createschema_gz -c ./tests/config/nextflow.config - tags: - - chewbbaca - - chewbbaca/createschema - files: - - path: output/chewbbaca/results/cds_coordinates.tsv - md5sum: e62f4e808939f97ccdbe4d17c1521b6c - - path: output/chewbbaca/results/invalid_cds.txt - md5sum: d0afbd9996054d8838e62dc3e852fa07 - - path: output/chewbbaca/results/test/.genes_list - contains: - - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ' - - path: output/chewbbaca/results/test/.schema_config - md5sum: 92b512f65fde7dce321ada54e5c431e9 - - path: output/chewbbaca/results/test/contigs-protein1.fasta - md5sum: 79f1e1c7105c0b34195e18c34960d2d4 - - path: output/chewbbaca/results/test/contigs-protein10.fasta - md5sum: 9fd40f7247cb3ed93f66828dbbfbac22 - - path: output/chewbbaca/results/test/contigs-protein14.fasta - md5sum: 2a8023e86fb119834f2d050daee33958 - - path: output/chewbbaca/results/test/contigs-protein16.fasta - md5sum: e006bb0da17f845c1672caed826d4ab7 - - path: output/chewbbaca/results/test/contigs-protein17.fasta - md5sum: 58f2501c0a7e48aaa86a87d01740b5c4 - - path: output/chewbbaca/results/test/contigs-protein18.fasta - md5sum: 6b4f385dc954df1fd2057a1c57872338 - - path: output/chewbbaca/results/test/contigs-protein19.fasta - md5sum: 3614c079d0b08f0c59bdaac9dcea0409 - - path: output/chewbbaca/results/test/contigs-protein2.fasta - md5sum: 0b982a66a0f001f11a86cc1b5a4ef80d - - path: output/chewbbaca/results/test/contigs-protein20.fasta - md5sum: 75b2492e5db0848079faafe6f60fe9fd - - path: output/chewbbaca/results/test/contigs-protein4.fasta - md5sum: 4ce5090bf2547bc588f0f8d00ae4a59d - - path: output/chewbbaca/results/test/contigs-protein6.fasta - md5sum: ffebf19b61285767a14f486af7181c30 - - path: output/chewbbaca/results/test/contigs-protein7.fasta - md5sum: ee06d9303c5b7844b003daa42b7a1869 - - path: output/chewbbaca/results/test/contigs-protein8.fasta - md5sum: 2a00efc36b036ab7f6c30f85533963cf - - path: output/chewbbaca/results/test/contigs-protein9.fasta - md5sum: ad9372b812030db327fa12d1e1731e85 - - path: output/chewbbaca/results/test/genome-protein1.fasta - md5sum: c1b28842a7e89e3bcc7d655afe51c609 - - path: output/chewbbaca/results/test/short/contigs-protein10_short.fasta - md5sum: 9fd40f7247cb3ed93f66828dbbfbac22 - - path: output/chewbbaca/results/test/short/contigs-protein14_short.fasta - md5sum: 2a8023e86fb119834f2d050daee33958 - - path: output/chewbbaca/results/test/short/contigs-protein16_short.fasta - md5sum: e006bb0da17f845c1672caed826d4ab7 - - path: output/chewbbaca/results/test/short/contigs-protein17_short.fasta - md5sum: 58f2501c0a7e48aaa86a87d01740b5c4 - - path: output/chewbbaca/results/test/short/contigs-protein18_short.fasta - md5sum: 6b4f385dc954df1fd2057a1c57872338 - - path: output/chewbbaca/results/test/short/contigs-protein19_short.fasta - md5sum: 3614c079d0b08f0c59bdaac9dcea0409 - - path: output/chewbbaca/results/test/short/contigs-protein1_short.fasta - md5sum: 79f1e1c7105c0b34195e18c34960d2d4 - - path: output/chewbbaca/results/test/short/contigs-protein20_short.fasta - md5sum: 75b2492e5db0848079faafe6f60fe9fd - - path: output/chewbbaca/results/test/short/contigs-protein2_short.fasta - md5sum: 0b982a66a0f001f11a86cc1b5a4ef80d - - path: output/chewbbaca/results/test/short/contigs-protein4_short.fasta - md5sum: 4ce5090bf2547bc588f0f8d00ae4a59d - - path: output/chewbbaca/results/test/short/contigs-protein6_short.fasta - md5sum: ffebf19b61285767a14f486af7181c30 - - path: output/chewbbaca/results/test/short/contigs-protein7_short.fasta - md5sum: ee06d9303c5b7844b003daa42b7a1869 - - path: output/chewbbaca/results/test/short/contigs-protein8_short.fasta - md5sum: 2a00efc36b036ab7f6c30f85533963cf - - path: output/chewbbaca/results/test/short/contigs-protein9_short.fasta - md5sum: ad9372b812030db327fa12d1e1731e85 - - path: output/chewbbaca/results/test/short/genome-protein1_short.fasta - md5sum: c1b28842a7e89e3bcc7d655afe51c609 - - path: output/chewbbaca/versions.yml From 744045587529d1e41b7158eec75f2a99ff43a7a0 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Sat, 6 Jan 2024 00:17:13 +0000 Subject: [PATCH 13/25] add stub and update tests, snapshot --- .../nf-core/chewbbaca/createschema/main.nf | 22 +- .../chewbbaca/createschema/tests/main.nf.test | 91 ++-- .../createschema/tests/main.nf.test.snap | 405 ++++++++++-------- .../createschema/tests/nextflow.config | 3 - 4 files changed, 290 insertions(+), 231 deletions(-) delete mode 100644 modules/nf-core/chewbbaca/createschema/tests/nextflow.config diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf index 4b9875869a2..d9d86ca9dc3 100644 --- a/modules/nf-core/chewbbaca/createschema/main.nf +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -13,10 +13,10 @@ process CHEWBBACA_CREATESCHEMA { path cds output: - tuple val(meta), path("results/$meta.id") , emit: schema - path "results/cds_coordinates.tsv" , emit: cds_coordinates - path "results/invalid_cds.txt" , emit: invalid_cds - path "versions.yml" , emit: versions + tuple val(meta), path("results/$meta.id") , emit: schema + path "results/cds_coordinates.tsv" , emit: cds_coordinates + path "results/invalid_cds.txt" , emit: invalid_cds + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -53,7 +53,19 @@ process CHEWBBACA_CREATESCHEMA { def schema = "--n ${prefix}" """ - mkdir -p results/$schema + mkdir -p results/$meta.id/short/ + touch results/$meta.id/contigs-protein{1..2}.fasta + touch results/$meta.id/contigs-protein{4..11}.fasta + touch results/$meta.id/contigs-protein{13..14}.fasta + touch results/$meta.id/contigs-protein{16..20}.fasta + touch results/$meta.id/.genes_list + touch results/$meta.id/.schema_config + touch results/$meta.id/short/contigs-protein{1..2}_short.fasta + touch results/$meta.id/short/contigs-protein{4..11}_short.fasta + touch results/$meta.id/short/contigs-protein{13..14}_short.fasta + touch results/$meta.id/short/contigs-protein{16..20}_short.fasta + touch results/cds_coordinates.tsv + touch results/invalid_cds.txt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test index e4ff159c51f..6d797fb1a56 100644 --- a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test +++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test @@ -9,19 +9,17 @@ nextflow_process { tag "chewbbaca" tag "chewbbaca/createschema" - test("test_chewbbaca_createschema_single") { + test("sarscov2 illumina contigs [fasta]") { when { process { - """ - - ptf = [] - cds = [] - input[0] = [[ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)] - input[1] = ptf - input[2] = cds + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) + ] + input[1] = [] // ptf + input[2] = [] //cds """ } } @@ -29,26 +27,26 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(file(process.out.schema[0][1]).list().sort().findAll { file(it).name != ".genes_list" }, + process.out.cds_coordinates, + process.out.invalid_cds, + process.out.versions).match() } ) } - } - test("test_chewbbaca_createschema_multi") { + test("sarscov2 illumina contigs & genome [fasta]") { when { process { - """ - - ptf = [] - cds = [] - input[0] = = [[ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] - input[1] = ptf - input[2] = cds + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + input[1] = [] // ptf + input[2] = [] // cds """ } } @@ -56,26 +54,54 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(file(process.out.schema[0][1]).list().sort().findAll { file(it).name != ".genes_list" }, + process.out.cds_coordinates, + process.out.invalid_cds, + process.out.versions).match() } ) } - } - test("test_chewbbaca_createschema_gz") { + test("sarscov2 illumina contigs [fasta] & genome [fasta_gz]") { when { process { - """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true) + ] + input[1] = [] // ptf + input[2] = [] // cds + """ + } + } - ptf = [] - cds = [] - input[0] = [[ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true)] - input[1] = ptf - input[2] = cds + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.schema[0][1]).list().sort().findAll { file(it).name != ".genes_list" }, + process.out.cds_coordinates, + process.out.invalid_cds, + process.out.versions).match() } + ) + } + } + + test("sarscov2 illumina contigs [fasta] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) + ] + input[1] = [] // ptf + input[2] = [] //cds """ } } @@ -86,6 +112,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } } diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap index 3f081e1d4ef..3abdd6b7fcc 100644 --- a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap +++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap @@ -1,227 +1,218 @@ { - "test_chewbbaca_createschema_gz": { + "sarscov2 illumina contigs [fasta]": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - ".genes_list:md5,2ffc5e37f87962d27169cfc3e20d1f96", - ".schema_config:md5,92b512f65fde7dce321ada54e5c431e9", - "contigs-protein1.fasta:md5,79f1e1c7105c0b34195e18c34960d2d4", - "contigs-protein10.fasta:md5,9fd40f7247cb3ed93f66828dbbfbac22", - "contigs-protein11.fasta:md5,b2f94d1babce56f5c1e46ccd35d2a7d7", - "contigs-protein13.fasta:md5,7314303d55a8598b229eca32ddeea14d", - "contigs-protein14.fasta:md5,2a8023e86fb119834f2d050daee33958", - "contigs-protein16.fasta:md5,e006bb0da17f845c1672caed826d4ab7", - "contigs-protein17.fasta:md5,58f2501c0a7e48aaa86a87d01740b5c4", - "contigs-protein18.fasta:md5,6b4f385dc954df1fd2057a1c57872338", - "contigs-protein19.fasta:md5,3614c079d0b08f0c59bdaac9dcea0409", - "contigs-protein2.fasta:md5,0b982a66a0f001f11a86cc1b5a4ef80d", - "contigs-protein20.fasta:md5,75b2492e5db0848079faafe6f60fe9fd", - "contigs-protein4.fasta:md5,4ce5090bf2547bc588f0f8d00ae4a59d", - "contigs-protein6.fasta:md5,ffebf19b61285767a14f486af7181c30", - "contigs-protein7.fasta:md5,ee06d9303c5b7844b003daa42b7a1869", - "contigs-protein8.fasta:md5,2a00efc36b036ab7f6c30f85533963cf", - "contigs-protein9.fasta:md5,ad9372b812030db327fa12d1e1731e85", - [ - "contigs-protein10_short.fasta:md5,9fd40f7247cb3ed93f66828dbbfbac22", - "contigs-protein11_short.fasta:md5,b2f94d1babce56f5c1e46ccd35d2a7d7", - "contigs-protein13_short.fasta:md5,7314303d55a8598b229eca32ddeea14d", - "contigs-protein14_short.fasta:md5,2a8023e86fb119834f2d050daee33958", - "contigs-protein16_short.fasta:md5,e006bb0da17f845c1672caed826d4ab7", - "contigs-protein17_short.fasta:md5,58f2501c0a7e48aaa86a87d01740b5c4", - "contigs-protein18_short.fasta:md5,6b4f385dc954df1fd2057a1c57872338", - "contigs-protein19_short.fasta:md5,3614c079d0b08f0c59bdaac9dcea0409", - "contigs-protein1_short.fasta:md5,79f1e1c7105c0b34195e18c34960d2d4", - "contigs-protein20_short.fasta:md5,75b2492e5db0848079faafe6f60fe9fd", - "contigs-protein2_short.fasta:md5,0b982a66a0f001f11a86cc1b5a4ef80d", - "contigs-protein4_short.fasta:md5,4ce5090bf2547bc588f0f8d00ae4a59d", - "contigs-protein6_short.fasta:md5,ffebf19b61285767a14f486af7181c30", - "contigs-protein7_short.fasta:md5,ee06d9303c5b7844b003daa42b7a1869", - "contigs-protein8_short.fasta:md5,2a00efc36b036ab7f6c30f85533963cf", - "contigs-protein9_short.fasta:md5,ad9372b812030db327fa12d1e1731e85" - ] - ] - ] - ], - "1": [ - "cds_coordinates.tsv:md5,7fef49207aa024b68f465e986f4c7444" - ], - "2": [ - "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" - ], - "3": [ - "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" - ], - "cds_coordinates": [ - "cds_coordinates.tsv:md5,7fef49207aa024b68f465e986f4c7444" - ], - "invalid_cds": [ - "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" - ], - "schema": [ - [ - { - "id": "test", - "single_end": false - }, - [ - ".genes_list:md5,2ffc5e37f87962d27169cfc3e20d1f96", - ".schema_config:md5,92b512f65fde7dce321ada54e5c431e9", - "contigs-protein1.fasta:md5,79f1e1c7105c0b34195e18c34960d2d4", - "contigs-protein10.fasta:md5,9fd40f7247cb3ed93f66828dbbfbac22", - "contigs-protein11.fasta:md5,b2f94d1babce56f5c1e46ccd35d2a7d7", - "contigs-protein13.fasta:md5,7314303d55a8598b229eca32ddeea14d", - "contigs-protein14.fasta:md5,2a8023e86fb119834f2d050daee33958", - "contigs-protein16.fasta:md5,e006bb0da17f845c1672caed826d4ab7", - "contigs-protein17.fasta:md5,58f2501c0a7e48aaa86a87d01740b5c4", - "contigs-protein18.fasta:md5,6b4f385dc954df1fd2057a1c57872338", - "contigs-protein19.fasta:md5,3614c079d0b08f0c59bdaac9dcea0409", - "contigs-protein2.fasta:md5,0b982a66a0f001f11a86cc1b5a4ef80d", - "contigs-protein20.fasta:md5,75b2492e5db0848079faafe6f60fe9fd", - "contigs-protein4.fasta:md5,4ce5090bf2547bc588f0f8d00ae4a59d", - "contigs-protein6.fasta:md5,ffebf19b61285767a14f486af7181c30", - "contigs-protein7.fasta:md5,ee06d9303c5b7844b003daa42b7a1869", - "contigs-protein8.fasta:md5,2a00efc36b036ab7f6c30f85533963cf", - "contigs-protein9.fasta:md5,ad9372b812030db327fa12d1e1731e85", - [ - "contigs-protein10_short.fasta:md5,9fd40f7247cb3ed93f66828dbbfbac22", - "contigs-protein11_short.fasta:md5,b2f94d1babce56f5c1e46ccd35d2a7d7", - "contigs-protein13_short.fasta:md5,7314303d55a8598b229eca32ddeea14d", - "contigs-protein14_short.fasta:md5,2a8023e86fb119834f2d050daee33958", - "contigs-protein16_short.fasta:md5,e006bb0da17f845c1672caed826d4ab7", - "contigs-protein17_short.fasta:md5,58f2501c0a7e48aaa86a87d01740b5c4", - "contigs-protein18_short.fasta:md5,6b4f385dc954df1fd2057a1c57872338", - "contigs-protein19_short.fasta:md5,3614c079d0b08f0c59bdaac9dcea0409", - "contigs-protein1_short.fasta:md5,79f1e1c7105c0b34195e18c34960d2d4", - "contigs-protein20_short.fasta:md5,75b2492e5db0848079faafe6f60fe9fd", - "contigs-protein2_short.fasta:md5,0b982a66a0f001f11a86cc1b5a4ef80d", - "contigs-protein4_short.fasta:md5,4ce5090bf2547bc588f0f8d00ae4a59d", - "contigs-protein6_short.fasta:md5,ffebf19b61285767a14f486af7181c30", - "contigs-protein7_short.fasta:md5,ee06d9303c5b7844b003daa42b7a1869", - "contigs-protein8_short.fasta:md5,2a00efc36b036ab7f6c30f85533963cf", - "contigs-protein9_short.fasta:md5,ad9372b812030db327fa12d1e1731e85" - ] - ] - ] - ], - "versions": [ - "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" - ] - } + [ + ".schema_config", + "contigs-protein1.fasta", + "contigs-protein10.fasta", + "contigs-protein11.fasta", + "contigs-protein13.fasta", + "contigs-protein14.fasta", + "contigs-protein16.fasta", + "contigs-protein17.fasta", + "contigs-protein18.fasta", + "contigs-protein19.fasta", + "contigs-protein2.fasta", + "contigs-protein20.fasta", + "contigs-protein4.fasta", + "contigs-protein6.fasta", + "contigs-protein7.fasta", + "contigs-protein8.fasta", + "contigs-protein9.fasta", + "short" + ], + [ + "cds_coordinates.tsv:md5,7fef49207aa024b68f465e986f4c7444" + ], + [ + "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" + ], + [ + "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" + ] ], - "timestamp": "2024-01-05T13:38:16.657917" + "timestamp": "2024-01-06T00:12:55.323150292" }, - "test_chewbbaca_createschema_single": { + "sarscov2 illumina contigs [fasta] & genome [fasta_gz]": { + "content": [ + [ + ".schema_config", + "contigs-protein1.fasta", + "contigs-protein10.fasta", + "contigs-protein11.fasta", + "contigs-protein13.fasta", + "contigs-protein14.fasta", + "contigs-protein16.fasta", + "contigs-protein17.fasta", + "contigs-protein18.fasta", + "contigs-protein19.fasta", + "contigs-protein2.fasta", + "contigs-protein20.fasta", + "contigs-protein4.fasta", + "contigs-protein6.fasta", + "contigs-protein7.fasta", + "contigs-protein8.fasta", + "contigs-protein9.fasta", + "short" + ], + [ + "cds_coordinates.tsv:md5,7fef49207aa024b68f465e986f4c7444" + ], + [ + "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" + ], + [ + "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" + ] + ], + "timestamp": "2024-01-06T00:13:27.65758787" + }, + "sarscov2 illumina contigs [fasta] - stub": { "content": [ { "0": [ [ { - "id": "test", + "id": 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] ], "1": [ - "cds_coordinates.tsv:md5,7fef49207aa024b68f465e986f4c7444" + "cds_coordinates.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], "2": [ - "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" + "invalid_cds.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], "3": [ "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" ], "cds_coordinates": [ - "cds_coordinates.tsv:md5,7fef49207aa024b68f465e986f4c7444" + "cds_coordinates.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], "invalid_cds": [ - "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" + "invalid_cds.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], "schema": [ [ { - "id": "test", + "id": [ + "contigs-protein1.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein10.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein11.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein13.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein14.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + 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"contigs-protein6.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein7.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein8.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein9.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", [ - "contigs-protein10_short.fasta:md5,9fd40f7247cb3ed93f66828dbbfbac22", - "contigs-protein11_short.fasta:md5,b2f94d1babce56f5c1e46ccd35d2a7d7", - "contigs-protein13_short.fasta:md5,7314303d55a8598b229eca32ddeea14d", - "contigs-protein14_short.fasta:md5,2a8023e86fb119834f2d050daee33958", - "contigs-protein16_short.fasta:md5,e006bb0da17f845c1672caed826d4ab7", - "contigs-protein17_short.fasta:md5,58f2501c0a7e48aaa86a87d01740b5c4", - "contigs-protein18_short.fasta:md5,6b4f385dc954df1fd2057a1c57872338", - "contigs-protein19_short.fasta:md5,3614c079d0b08f0c59bdaac9dcea0409", - "contigs-protein1_short.fasta:md5,79f1e1c7105c0b34195e18c34960d2d4", - "contigs-protein20_short.fasta:md5,75b2492e5db0848079faafe6f60fe9fd", - 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"contigs-protein1_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein20_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein2_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein4_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein5_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein6_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein7_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein8_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs-protein9_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ] @@ -231,6 +222,40 @@ ] } ], - "timestamp": "2024-01-05T13:37:51.898568" + "timestamp": "2024-01-06T00:13:42.537101451" + }, + "sarscov2 illumina contigs & genome [fasta]": { + "content": [ + [ + ".schema_config", + "contigs-protein1.fasta", + "contigs-protein10.fasta", + "contigs-protein11.fasta", + "contigs-protein13.fasta", + "contigs-protein14.fasta", + "contigs-protein16.fasta", + "contigs-protein17.fasta", + "contigs-protein18.fasta", + "contigs-protein19.fasta", + "contigs-protein2.fasta", + "contigs-protein20.fasta", + "contigs-protein4.fasta", + "contigs-protein6.fasta", + "contigs-protein7.fasta", + "contigs-protein8.fasta", + "contigs-protein9.fasta", + "short" + ], + [ + "cds_coordinates.tsv:md5,7fef49207aa024b68f465e986f4c7444" + ], + [ + "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" + ], + [ + "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" + ] + ], + "timestamp": "2024-01-06T00:13:11.663353018" } } \ No newline at end of file diff --git a/modules/nf-core/chewbbaca/createschema/tests/nextflow.config b/modules/nf-core/chewbbaca/createschema/tests/nextflow.config deleted file mode 100644 index 0293c16f9ee..00000000000 --- a/modules/nf-core/chewbbaca/createschema/tests/nextflow.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } -} From bf830ed7c00bcdca6287bceea291437c6cbd707f Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Mon, 8 Jan 2024 12:48:46 -0800 Subject: [PATCH 14/25] updated stub --- modules/nf-core/chewbbaca/createschema/main.nf | 10 ++-------- .../nf-core/chewbbaca/createschema/tests/main.nf.test | 5 ++++- 2 files changed, 6 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf index d9d86ca9dc3..c61579f9f75 100644 --- a/modules/nf-core/chewbbaca/createschema/main.nf +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -54,16 +54,10 @@ process CHEWBBACA_CREATESCHEMA { """ mkdir -p results/$meta.id/short/ - touch results/$meta.id/contigs-protein{1..2}.fasta - touch results/$meta.id/contigs-protein{4..11}.fasta - touch results/$meta.id/contigs-protein{13..14}.fasta - touch results/$meta.id/contigs-protein{16..20}.fasta + touch results/$meta.id/contigs-protein{1..*}.fasta touch results/$meta.id/.genes_list touch results/$meta.id/.schema_config - touch results/$meta.id/short/contigs-protein{1..2}_short.fasta - touch results/$meta.id/short/contigs-protein{4..11}_short.fasta - touch results/$meta.id/short/contigs-protein{13..14}_short.fasta - touch results/$meta.id/short/contigs-protein{16..20}_short.fasta + touch results/$meta.id/short/contigs-protein{1..*}_short.fasta touch results/cds_coordinates.tsv touch results/invalid_cds.txt diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test index 6d797fb1a56..2841fa90f5d 100644 --- a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test +++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test @@ -109,7 +109,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(file(process.out.schema[0][1]).list().sort().findAll { file(it).name != ".genes_list" }, + process.out.cds_coordinates, + process.out.invalid_cds, + process.out.versions).match() } ) } } From 447baeec7c557765c92ce74a2e50f2dfc35cb288 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Mon, 8 Jan 2024 13:32:47 -0800 Subject: [PATCH 15/25] update stub test --- .../chewbbaca/createschema/tests/main.nf.test | 7 +- .../createschema/tests/main.nf.test.snap | 170 ++---------------- 2 files changed, 20 insertions(+), 157 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test index 2841fa90f5d..28853f4df52 100644 --- a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test +++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test @@ -89,7 +89,7 @@ nextflow_process { } } - test("sarscov2 illumina contigs [fasta] - stub") { + test("sarscov2 illumina contigs [fasta] & genome [fasta_gz] - stub") { options "-stub" @@ -98,10 +98,11 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true) ] input[1] = [] // ptf - input[2] = [] //cds + input[2] = [] // cds """ } } diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap index 3abdd6b7fcc..2656112599a 100644 --- a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap +++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap @@ -67,162 +67,24 @@ ], "timestamp": "2024-01-06T00:13:27.65758787" }, - "sarscov2 illumina contigs [fasta] - stub": { + "sarscov2 illumina contigs [fasta] & genome [fasta_gz] - stub": { "content": [ - { - "0": [ - [ - { - "id": [ - "contigs-protein1.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein10.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein11.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein13.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein14.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein16.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein17.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein18.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein19.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein2.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein20.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein4.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein5.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein6.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein7.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein8.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein9.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "single_end": false - }, - [ - ".genes_list:md5,d41d8cd98f00b204e9800998ecf8427e", - ".schema_config:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein1.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein10.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein11.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein13.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein14.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein16.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein17.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein18.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein19.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein2.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein20.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein4.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein5.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein6.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein7.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein8.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein9.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - [ - "contigs-protein10_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein11_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein13_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein14_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein16_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein17_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein18_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein19_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein1_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein20_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein2_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein4_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein5_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein6_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein7_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein8_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein9_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ] - ], - "1": [ - "cds_coordinates.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "2": [ - "invalid_cds.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "3": [ - "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" - ], - "cds_coordinates": [ - "cds_coordinates.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "invalid_cds": [ - "invalid_cds.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "schema": [ - [ - { - "id": [ - "contigs-protein1.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein10.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein11.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein13.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein14.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein16.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein17.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein18.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein19.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein2.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein20.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein4.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein5.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein6.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein7.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein8.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein9.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "single_end": false - }, - [ - ".genes_list:md5,d41d8cd98f00b204e9800998ecf8427e", - ".schema_config:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein1.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein10.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein11.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein13.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein14.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein16.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein17.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein18.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein19.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein2.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein20.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein4.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein5.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein6.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein7.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein8.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein9.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - [ - "contigs-protein10_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein11_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein13_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein14_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein16_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein17_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein18_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein19_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein1_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein20_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein2_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein4_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein5_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein6_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein7_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein8_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "contigs-protein9_short.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ] - ], - "versions": [ - "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" - ] - } + [ + ".schema_config", + "contigs-protein{1..*}.fasta", + "short" + ], + [ + "cds_coordinates.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "invalid_cds.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" + ] ], - "timestamp": "2024-01-06T00:13:42.537101451" + "timestamp": "2024-01-08T13:24:00.874811" }, "sarscov2 illumina contigs & genome [fasta]": { "content": [ From 210db7abce91029a1e932df57acce0b81a018616 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Mon, 8 Jan 2024 14:23:54 -0800 Subject: [PATCH 16/25] update stub test --- .../chewbbaca/createschema/tests/main.nf.test.snap | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap index 2656112599a..1552d67edad 100644 --- a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap +++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap @@ -31,7 +31,7 @@ "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" ] ], - "timestamp": "2024-01-06T00:12:55.323150292" + "timestamp": "2024-01-08T13:40:20.083917" }, "sarscov2 illumina contigs [fasta] & genome [fasta_gz]": { "content": [ @@ -65,7 +65,7 @@ "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" ] ], - "timestamp": "2024-01-06T00:13:27.65758787" + "timestamp": "2024-01-08T13:40:52.243835" }, "sarscov2 illumina contigs [fasta] & genome [fasta_gz] - stub": { "content": [ @@ -84,7 +84,7 @@ "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" ] ], - "timestamp": "2024-01-08T13:24:00.874811" + "timestamp": "2024-01-08T13:41:03.324402" }, "sarscov2 illumina contigs & genome [fasta]": { "content": [ @@ -118,6 +118,6 @@ "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" ] ], - "timestamp": "2024-01-06T00:13:11.663353018" + "timestamp": "2024-01-08T13:40:35.954748" } } \ No newline at end of file From ac04372ab8697a397c5a70f9b5cd91d7283f4282 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Wed, 24 Jan 2024 22:42:12 -0800 Subject: [PATCH 17/25] bump the version --- modules/nf-core/chewbbaca/createschema/environment.yml | 2 +- modules/nf-core/chewbbaca/createschema/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/environment.yml b/modules/nf-core/chewbbaca/createschema/environment.yml index 9788ebbccfa..ef2d8e4bc53 100644 --- a/modules/nf-core/chewbbaca/createschema/environment.yml +++ b/modules/nf-core/chewbbaca/createschema/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::chewbbaca=3.3.1 + - bioconda::chewbbaca=3.3.2 diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf index c61579f9f75..fab9c3a41f9 100644 --- a/modules/nf-core/chewbbaca/createschema/main.nf +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -4,8 +4,8 @@ process CHEWBBACA_CREATESCHEMA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/chewbbaca:3.3.1--pyhdfd78af_0': - 'biocontainers/chewbbaca:3.3.1--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/chewbbaca:3.3.2--pyhdfd78af_0': + 'biocontainers/chewbbaca:3.3.2--pyhdfd78af_0' }" input: tuple val(meta), path(fasta, stageAs: "input_genomes/*") From 77c6a38860636dc66e5036608da4cd339a20d680 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Wed, 24 Jan 2024 23:50:01 -0800 Subject: [PATCH 18/25] update --- modules/nf-core/chewbbaca/createschema/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf index fab9c3a41f9..8681d00ffa1 100644 --- a/modules/nf-core/chewbbaca/createschema/main.nf +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -5,7 +5,7 @@ process CHEWBBACA_CREATESCHEMA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/chewbbaca:3.3.2--pyhdfd78af_0': - 'biocontainers/chewbbaca:3.3.2--pyhdfd78af_0' }" + 'biocontainers/chewbbaca:3.3.2--pyhdfd78af' }" input: tuple val(meta), path(fasta, stageAs: "input_genomes/*") From 8c8955085b3491c91e7853ae68d4ef59d1b8234f Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Fri, 26 Jan 2024 09:53:01 -0800 Subject: [PATCH 19/25] updating container version --- modules/nf-core/chewbbaca/createschema/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf index 8681d00ffa1..fab9c3a41f9 100644 --- a/modules/nf-core/chewbbaca/createschema/main.nf +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -5,7 +5,7 @@ process CHEWBBACA_CREATESCHEMA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/chewbbaca:3.3.2--pyhdfd78af_0': - 'biocontainers/chewbbaca:3.3.2--pyhdfd78af' }" + 'biocontainers/chewbbaca:3.3.2--pyhdfd78af_0' }" input: tuple val(meta), path(fasta, stageAs: "input_genomes/*") From fc2322038bfd9bbeaecfc59b2d9a5368f5555246 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Fri, 26 Jan 2024 12:02:50 -0800 Subject: [PATCH 20/25] updated test snapshot --- .../createschema/tests/main.nf.test.snap | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap index 1552d67edad..39bc86987dc 100644 --- a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap +++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap @@ -28,10 +28,10 @@ "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" ], [ - "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" + "versions.yml:md5,b81657e89125c6fe743155b58d331e0c" ] ], - "timestamp": "2024-01-08T13:40:20.083917" + "timestamp": "2024-01-26T10:59:57.581710475" }, "sarscov2 illumina contigs [fasta] & genome [fasta_gz]": { "content": [ @@ -62,10 +62,10 @@ "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" ], [ - "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" + "versions.yml:md5,c5753fc5c2376d5b7991a16e7412913c" ] ], - "timestamp": "2024-01-08T13:40:52.243835" + "timestamp": "2024-01-26T11:17:48.49018737" }, "sarscov2 illumina contigs [fasta] & genome [fasta_gz] - stub": { "content": [ @@ -81,10 +81,10 @@ "invalid_cds.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ - "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" + "versions.yml:md5,71ad745d6906275995c08db54598385b" ] ], - "timestamp": "2024-01-08T13:41:03.324402" + "timestamp": "2024-01-26T11:25:40.05202056" }, "sarscov2 illumina contigs & genome [fasta]": { "content": [ @@ -115,9 +115,9 @@ "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" ], [ - "versions.yml:md5,e0e902ceb5a8444ef440c4ec66e46be6" + "versions.yml:md5,1843484a5df6233a61c7e59f884e3474" ] ], - "timestamp": "2024-01-08T13:40:35.954748" + "timestamp": "2024-01-26T11:09:35.499653829" } } \ No newline at end of file From f03ed0d5e31103e2ff32df44036b5b0b0e207a43 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Fri, 26 Jan 2024 12:19:03 -0800 Subject: [PATCH 21/25] updated nf-test snapshot --- .../createschema/tests/main.nf.test.snap | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap index 39bc86987dc..bac933bb36f 100644 --- a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap +++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap @@ -28,10 +28,10 @@ "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" ], [ - "versions.yml:md5,b81657e89125c6fe743155b58d331e0c" + "versions.yml:md5,cc97e7dbcf8455a4bf166f0bf326e769" ] ], - "timestamp": "2024-01-26T10:59:57.581710475" + "timestamp": "2024-01-26T12:13:29.558920352" }, "sarscov2 illumina contigs [fasta] & genome [fasta_gz]": { "content": [ @@ -62,10 +62,10 @@ "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" ], [ - "versions.yml:md5,c5753fc5c2376d5b7991a16e7412913c" + "versions.yml:md5,cc97e7dbcf8455a4bf166f0bf326e769" ] ], - "timestamp": "2024-01-26T11:17:48.49018737" + "timestamp": "2024-01-26T12:14:01.738666237" }, "sarscov2 illumina contigs [fasta] & genome [fasta_gz] - stub": { "content": [ @@ -81,10 +81,10 @@ "invalid_cds.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ - "versions.yml:md5,71ad745d6906275995c08db54598385b" + "versions.yml:md5,cc97e7dbcf8455a4bf166f0bf326e769" ] ], - "timestamp": "2024-01-26T11:25:40.05202056" + "timestamp": "2024-01-26T12:14:12.757130114" }, "sarscov2 illumina contigs & genome [fasta]": { "content": [ @@ -115,9 +115,9 @@ "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" ], [ - "versions.yml:md5,1843484a5df6233a61c7e59f884e3474" + "versions.yml:md5,cc97e7dbcf8455a4bf166f0bf326e769" ] ], - "timestamp": "2024-01-26T11:09:35.499653829" + "timestamp": "2024-01-26T12:13:45.580057569" } } \ No newline at end of file From fc6abd08f36106d51f8e0c7b5769088432586d91 Mon Sep 17 00:00:00 2001 From: Zohaib Anwar Date: Tue, 30 Jan 2024 00:06:32 -0800 Subject: [PATCH 22/25] added libmamba to environment file --- modules/nf-core/chewbbaca/createschema/environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/chewbbaca/createschema/environment.yml b/modules/nf-core/chewbbaca/createschema/environment.yml index ef2d8e4bc53..b194eca2dfe 100644 --- a/modules/nf-core/chewbbaca/createschema/environment.yml +++ b/modules/nf-core/chewbbaca/createschema/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: + - libmamba - bioconda::chewbbaca=3.3.2 From 736b183dd474c1b6331edf53c8acd0aa0b8195f9 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Tue, 11 Jun 2024 18:10:45 +0000 Subject: [PATCH 23/25] Fix tests and linting --- .../chewbbaca/createschema/environment.yml | 4 +- .../nf-core/chewbbaca/createschema/main.nf | 4 +- .../nf-core/chewbbaca/createschema/meta.yml | 6 +-- .../createschema/tests/main.nf.test.snap | 38 +++++++++++++------ 4 files changed, 35 insertions(+), 17 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/environment.yml b/modules/nf-core/chewbbaca/createschema/environment.yml index b194eca2dfe..9b5924e1aa0 100644 --- a/modules/nf-core/chewbbaca/createschema/environment.yml +++ b/modules/nf-core/chewbbaca/createschema/environment.yml @@ -1,8 +1,10 @@ name: chewbbaca_createschema + channels: - conda-forge - bioconda - defaults + dependencies: + - bioconda::chewbbaca=3.3.5 - libmamba - - bioconda::chewbbaca=3.3.2 diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf index fab9c3a41f9..88c653a5594 100644 --- a/modules/nf-core/chewbbaca/createschema/main.nf +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -4,8 +4,8 @@ process CHEWBBACA_CREATESCHEMA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/chewbbaca:3.3.2--pyhdfd78af_0': - 'biocontainers/chewbbaca:3.3.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/chewbbaca:3.3.5--pyhdfd78af_0': + 'biocontainers/chewbbaca:3.3.5--pyhdfd78af_0' }" input: tuple val(meta), path(fasta, stageAs: "input_genomes/*") diff --git a/modules/nf-core/chewbbaca/createschema/meta.yml b/modules/nf-core/chewbbaca/createschema/meta.yml index 0b3a4c369cc..c0dbbea1efd 100644 --- a/modules/nf-core/chewbbaca/createschema/meta.yml +++ b/modules/nf-core/chewbbaca/createschema/meta.yml @@ -47,17 +47,17 @@ output: Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]` - - schema_dir: + - schema: type: directory description: schema directory pattern: "*/" - - tsv: + - cds_coordinates: type: file description: file contains the coordinates of the CDS in the input sample pattern: "*_cds_coordinates.tsv" - - txt: + - invalid_cds: type: file description: file contains the list of alleles predicted by Prodigal that were excluded pattern: "*_invalid_cds.txt" diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap index bac933bb36f..85e63be9af5 100644 --- a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap +++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test.snap @@ -25,13 +25,17 @@ "cds_coordinates.tsv:md5,7fef49207aa024b68f465e986f4c7444" ], [ - "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" + "invalid_cds.txt:md5,0d1ae99b034deaca2b04e64ed7548d18" ], [ - "versions.yml:md5,cc97e7dbcf8455a4bf166f0bf326e769" + "versions.yml:md5,a957a2c9e352caa39f8e12608b287810" ] ], - "timestamp": "2024-01-26T12:13:29.558920352" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-11T09:38:07.580722145" }, "sarscov2 illumina contigs [fasta] & genome [fasta_gz]": { "content": [ @@ -59,13 +63,17 @@ "cds_coordinates.tsv:md5,7fef49207aa024b68f465e986f4c7444" ], [ - "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" + "invalid_cds.txt:md5,0d1ae99b034deaca2b04e64ed7548d18" ], [ - "versions.yml:md5,cc97e7dbcf8455a4bf166f0bf326e769" + "versions.yml:md5,a957a2c9e352caa39f8e12608b287810" ] ], - "timestamp": "2024-01-26T12:14:01.738666237" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-11T09:38:46.431200697" }, "sarscov2 illumina contigs [fasta] & genome [fasta_gz] - stub": { "content": [ @@ -81,10 +89,14 @@ "invalid_cds.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ - "versions.yml:md5,cc97e7dbcf8455a4bf166f0bf326e769" + "versions.yml:md5,a957a2c9e352caa39f8e12608b287810" ] ], - "timestamp": "2024-01-26T12:14:12.757130114" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-11T09:39:14.063620184" }, "sarscov2 illumina contigs & genome [fasta]": { "content": [ @@ -112,12 +124,16 @@ "cds_coordinates.tsv:md5,7fef49207aa024b68f465e986f4c7444" ], [ - "invalid_cds.txt:md5,d0afbd9996054d8838e62dc3e852fa07" + "invalid_cds.txt:md5,0d1ae99b034deaca2b04e64ed7548d18" ], [ - "versions.yml:md5,cc97e7dbcf8455a4bf166f0bf326e769" + "versions.yml:md5,a957a2c9e352caa39f8e12608b287810" ] ], - "timestamp": "2024-01-26T12:13:45.580057569" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-11T09:38:24.00163744" } } \ No newline at end of file From 7c6cf543ccd6b8783f956c940b593ee4b2820d64 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Tue, 2 Jul 2024 16:10:43 +0100 Subject: [PATCH 24/25] Update modules/nf-core/chewbbaca/createschema/main.nf Co-authored-by: Jose Espinosa-Carrasco --- modules/nf-core/chewbbaca/createschema/main.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf index 88c653a5594..90ca4ae4532 100644 --- a/modules/nf-core/chewbbaca/createschema/main.nf +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -13,10 +13,10 @@ process CHEWBBACA_CREATESCHEMA { path cds output: - tuple val(meta), path("results/$meta.id") , emit: schema - path "results/cds_coordinates.tsv" , emit: cds_coordinates - path "results/invalid_cds.txt" , emit: invalid_cds - path "versions.yml" , emit: versions + tuple val(meta), path("results/$meta.id"), emit: schema + path "results/cds_coordinates.tsv" , emit: cds_coordinates + path "results/invalid_cds.txt" , emit: invalid_cds + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when From 9131d1e6a0bd71fe5c943554c15f41c600f31c35 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Tue, 2 Jul 2024 16:11:13 +0100 Subject: [PATCH 25/25] Apply suggestions from code review Co-authored-by: Jose Espinosa-Carrasco --- modules/nf-core/chewbbaca/createschema/meta.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/chewbbaca/createschema/meta.yml b/modules/nf-core/chewbbaca/createschema/meta.yml index c0dbbea1efd..1c7be66e2ea 100644 --- a/modules/nf-core/chewbbaca/createschema/meta.yml +++ b/modules/nf-core/chewbbaca/createschema/meta.yml @@ -49,17 +49,17 @@ output: - schema: type: directory - description: schema directory + description: Schema directory pattern: "*/" - cds_coordinates: type: file - description: file contains the coordinates of the CDS in the input sample + description: File containing the coordinates of the CDS in the input sample pattern: "*_cds_coordinates.tsv" - invalid_cds: type: file - description: file contains the list of alleles predicted by Prodigal that were excluded + description: File containing the list of alleles predicted by Prodigal that were excluded pattern: "*_invalid_cds.txt" authors: