From c27498285a0beca2239b395cf88129c586a837fc Mon Sep 17 00:00:00 2001 From: poddarharsh15 <45700858+poddarharsh15@users.noreply.github.com> Date: Mon, 8 Jul 2024 14:52:09 +0200 Subject: [PATCH] dysgu==1.6.4_version update (#5928) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * all_files_update * Update environment.yml * update_meta.yml * input==input_bam * update_snapshot * meta.yml,tags.yml update * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * update_author --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --- modules/nf-core/dysgu/environment.yml | 7 ++ modules/nf-core/dysgu/main.nf | 55 +++++++++++ modules/nf-core/dysgu/meta.yml | 68 +++++++++++++ modules/nf-core/dysgu/tests/main.nf.test | 96 +++++++++++++++++++ modules/nf-core/dysgu/tests/main.nf.test.snap | 75 +++++++++++++++ modules/nf-core/dysgu/tests/nextflow.config | 5 + modules/nf-core/dysgu/tests/tags.yml | 2 + 7 files changed, 308 insertions(+) create mode 100644 modules/nf-core/dysgu/environment.yml create mode 100644 modules/nf-core/dysgu/main.nf create mode 100644 modules/nf-core/dysgu/meta.yml create mode 100644 modules/nf-core/dysgu/tests/main.nf.test create mode 100644 modules/nf-core/dysgu/tests/main.nf.test.snap create mode 100644 modules/nf-core/dysgu/tests/nextflow.config create mode 100644 modules/nf-core/dysgu/tests/tags.yml diff --git a/modules/nf-core/dysgu/environment.yml b/modules/nf-core/dysgu/environment.yml new file mode 100644 index 00000000000..5efb6db61ad --- /dev/null +++ b/modules/nf-core/dysgu/environment.yml @@ -0,0 +1,7 @@ +name: dysgu +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - dysgu diff --git a/modules/nf-core/dysgu/main.nf b/modules/nf-core/dysgu/main.nf new file mode 100644 index 00000000000..6aa1deea958 --- /dev/null +++ b/modules/nf-core/dysgu/main.nf @@ -0,0 +1,55 @@ +process DYSGU { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'oras://community.wave.seqera.io/library/dysgu:48830f55112c399e': + 'community.wave.seqera.io/library/dysgu:faf71ac972284412' }" + + input: + tuple val(meta), path(input), path(index) + tuple val(meta2), path(fasta), path(fai) + + output: + tuple val(meta), path('*.vcf.gz') , emit: vcf + tuple val(meta), path('*.vcf.gz.tbi') , emit: tbi + path 'versions.yml' , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + dysgu run \\ + -p ${task.cpus} \\ + -x \\ + $fasta \\ + . \\ + $input \\ + | bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz + tabix ${args3} ${prefix}.vcf.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + dysgu: \$(dysgu --version 2>&1) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "" | gzip > ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + dysgu: \$(dysgu --version 2>&1) + END_VERSIONS + """ +} diff --git a/modules/nf-core/dysgu/meta.yml b/modules/nf-core/dysgu/meta.yml new file mode 100644 index 00000000000..67c6c70abf8 --- /dev/null +++ b/modules/nf-core/dysgu/meta.yml @@ -0,0 +1,68 @@ +name: dysgu + +description: Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations. +keywords: + - structural variants + - sv + - vcf +tools: + - dysgu: + description: Structural variant caller for mapped sequencing data + homepage: https://github.com/kcleal/dysgu + documentation: https://github.com/kcleal/dysgu/blob/master/README.rst + tool_dev_url: https://github.com/kcleal/dysgu + doi: "10.1093/nar/gkac039" + licence: ["GPL-3.0-or-later"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - input: + type: file + description: Input BAM file + pattern: "*.bam" + - index: + type: file + description: BAM index file + pattern: "*.bai" + - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - vcf: + type: file + description: VCF file with identified structural variants + pattern: "*.{vcf.gz}" + - tbi: + type: file + description: The index of the BCF/VCF file + pattern: "*.{vcf.gz.tbi}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@famosab" + - "@poddarharsh15" +maintainers: + - "@poddarharsh15" diff --git a/modules/nf-core/dysgu/tests/main.nf.test b/modules/nf-core/dysgu/tests/main.nf.test new file mode 100644 index 00000000000..1714b5b7ab3 --- /dev/null +++ b/modules/nf-core/dysgu/tests/main.nf.test @@ -0,0 +1,96 @@ +nextflow_process { + + name "Test Process DYSGU" + script "../main.nf" + process "DYSGU" + config "./nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "dysgu" + + + test("human - bam") { + + when { + process { + """ + input[0] = [ [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ [ id:'reference'], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") } + ) + } + + } + + + test("human - cram") { + + when { + process { + """ + input[0] = [ [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) + ] + input[1] = [ [ id:'reference'], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") } + ) + } + + } + + + test("human - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ [ id:'reference'], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/dysgu/tests/main.nf.test.snap b/modules/nf-core/dysgu/tests/main.nf.test.snap new file mode 100644 index 00000000000..ecf725f5d30 --- /dev/null +++ b/modules/nf-core/dysgu/tests/main.nf.test.snap @@ -0,0 +1,75 @@ +{ + "human - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,cf1e0487502108690603dd16f034bf5e" + ], + "tbi": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,cf1e0487502108690603dd16f034bf5e" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-08T13:18:45.660262" + }, + "human - bam": { + "content": [ + [ + "versions.yml:md5,cf1e0487502108690603dd16f034bf5e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-08T13:19:56.62312" + }, + "human - cram": { + "content": [ + [ + "versions.yml:md5,cf1e0487502108690603dd16f034bf5e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-08T13:20:04.494134" + } +} \ No newline at end of file diff --git a/modules/nf-core/dysgu/tests/nextflow.config b/modules/nf-core/dysgu/tests/nextflow.config new file mode 100644 index 00000000000..5336ab55cf4 --- /dev/null +++ b/modules/nf-core/dysgu/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: DYSGU { + ext.args = '--exome ' + } +} \ No newline at end of file diff --git a/modules/nf-core/dysgu/tests/tags.yml b/modules/nf-core/dysgu/tests/tags.yml new file mode 100644 index 00000000000..6bffc95e916 --- /dev/null +++ b/modules/nf-core/dysgu/tests/tags.yml @@ -0,0 +1,2 @@ +dysgu: + - "modules/nf-core/dysgu/**"