From 3ddbcf437eb68fc9d821ceb36c6338523d4b5a42 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 21 Apr 2022 17:24:29 +0100 Subject: [PATCH 1/3] Rename process from STRINGTIE to STRINGTIE_STRINGTIE --- modules/stringtie/stringtie/main.nf | 2 +- tests/modules/stringtie/stringtie/main.nf | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/stringtie/stringtie/main.nf b/modules/stringtie/stringtie/main.nf index f37e347a50b..cd0627ac9dc 100644 --- a/modules/stringtie/stringtie/main.nf +++ b/modules/stringtie/stringtie/main.nf @@ -1,4 +1,4 @@ -process STRINGTIE { +process STRINGTIE_STRINGTIE { tag "$meta.id" label 'process_medium' diff --git a/tests/modules/stringtie/stringtie/main.nf b/tests/modules/stringtie/stringtie/main.nf index ae6abe67294..463e4b98183 100644 --- a/tests/modules/stringtie/stringtie/main.nf +++ b/tests/modules/stringtie/stringtie/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' +include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' // // Test with forward strandedness // @@ -13,7 +13,7 @@ workflow test_stringtie_forward { ] annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - STRINGTIE ( input, annotation_gtf ) + STRINGTIE_STRINGTIE ( input, annotation_gtf ) } // @@ -26,5 +26,5 @@ workflow test_stringtie_reverse { ] annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - STRINGTIE ( input, annotation_gtf ) + STRINGTIE_STRINGTIE ( input, annotation_gtf ) } From 5c03d5cf148fd0a353c9e4e8281b56538c82b20c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 21 Apr 2022 17:32:49 +0100 Subject: [PATCH 2/3] Bump Stringtie version to 2.2.1 and remove empty files in tests --- modules/stringtie/merge/main.nf | 6 +++--- modules/stringtie/stringtie/main.nf | 6 +++--- modules/stringtie/stringtie/meta.yml | 2 +- tests/modules/stringtie/merge/test.yml | 2 -- tests/modules/stringtie/stringtie/test.yml | 2 -- 5 files changed, 7 insertions(+), 11 deletions(-) diff --git a/modules/stringtie/merge/main.nf b/modules/stringtie/merge/main.nf index aa11eb36e1b..c8460c942e8 100644 --- a/modules/stringtie/merge/main.nf +++ b/modules/stringtie/merge/main.nf @@ -2,10 +2,10 @@ process STRINGTIE_MERGE { label 'process_medium' // Note: 2.7X indices incompatible with AWS iGenomes. - conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null) + conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' : - 'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }" + 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : + 'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }" input: path stringtie_gtf diff --git a/modules/stringtie/stringtie/main.nf b/modules/stringtie/stringtie/main.nf index cd0627ac9dc..c70c9819a7e 100644 --- a/modules/stringtie/stringtie/main.nf +++ b/modules/stringtie/stringtie/main.nf @@ -2,10 +2,10 @@ process STRINGTIE_STRINGTIE { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null) + conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' : - 'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }" + 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : + 'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }" input: tuple val(meta), path(bam) diff --git a/modules/stringtie/stringtie/meta.yml b/modules/stringtie/stringtie/meta.yml index a462c574e12..0dda84d041c 100644 --- a/modules/stringtie/stringtie/meta.yml +++ b/modules/stringtie/stringtie/meta.yml @@ -1,4 +1,4 @@ -name: stringtie +name: stringtie_stringtie description: Transcript assembly and quantification for RNA-Se keywords: - transcript diff --git a/tests/modules/stringtie/merge/test.yml b/tests/modules/stringtie/merge/test.yml index 392a1d7cc3f..8183a11688c 100644 --- a/tests/modules/stringtie/merge/test.yml +++ b/tests/modules/stringtie/merge/test.yml @@ -17,7 +17,6 @@ - path: output/stringtie/test.ballgown/t_data.ctab md5sum: 92a98902784e7406ffe054d2adbabc7c - path: output/stringtie/test.coverage.gtf - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: output/stringtie/test.gene.abundance.txt md5sum: 9708811bcefe0f6384293d6f419f3250 - path: output/stringtie/test.transcripts.gtf @@ -42,7 +41,6 @@ - path: output/stringtie/test.ballgown/t_data.ctab md5sum: 92a98902784e7406ffe054d2adbabc7c - path: output/stringtie/test.coverage.gtf - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: output/stringtie/test.gene.abundance.txt md5sum: 94b85145d60ab1b80a7f0f6cf08418b0 - path: output/stringtie/test.transcripts.gtf diff --git a/tests/modules/stringtie/stringtie/test.yml b/tests/modules/stringtie/stringtie/test.yml index 732b9fd146e..2815ba8194a 100644 --- a/tests/modules/stringtie/stringtie/test.yml +++ b/tests/modules/stringtie/stringtie/test.yml @@ -8,7 +8,6 @@ - path: ./output/stringtie/test.gene.abundance.txt md5sum: 7d8bce7f2a922e367cedccae7267c22e - path: ./output/stringtie/test.coverage.gtf - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: ./output/stringtie/test.ballgown/e_data.ctab md5sum: 6b4cf69bc03f3f69890f972a0e8b7471 - path: ./output/stringtie/test.ballgown/i_data.ctab @@ -30,7 +29,6 @@ - path: ./output/stringtie/test.gene.abundance.txt md5sum: 7385b870b955dae2c2ab78a70cf05cce - path: ./output/stringtie/test.coverage.gtf - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: ./output/stringtie/test.ballgown/e_data.ctab md5sum: 879b6696029d19c4737b562e9d149218 - path: ./output/stringtie/test.ballgown/i_data.ctab From ba1ddbc3db338a012b2f563a846577215a818ea8 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 21 Apr 2022 17:39:30 +0100 Subject: [PATCH 3/3] Fix tests for stringtie/merge --- tests/modules/stringtie/merge/main.nf | 12 ++++++------ tests/modules/stringtie/merge/test.yml | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/tests/modules/stringtie/merge/main.nf b/tests/modules/stringtie/merge/main.nf index 7851e755d22..3fe32902595 100644 --- a/tests/modules/stringtie/merge/main.nf +++ b/tests/modules/stringtie/merge/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' -include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf' +include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' +include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf' /* * Test with forward strandedness @@ -15,8 +15,8 @@ workflow test_stringtie_forward_merge { ] annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) - STRINGTIE ( input, annotation_gtf ) - STRINGTIE + STRINGTIE_STRINGTIE ( input, annotation_gtf ) + STRINGTIE_STRINGTIE .out .transcript_gtf .map { it -> it[1] } @@ -35,8 +35,8 @@ workflow test_stringtie_reverse_merge { ] annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) - STRINGTIE ( input, annotation_gtf ) - STRINGTIE + STRINGTIE_STRINGTIE ( input, annotation_gtf ) + STRINGTIE_STRINGTIE .out .transcript_gtf .map { it -> it[1] } diff --git a/tests/modules/stringtie/merge/test.yml b/tests/modules/stringtie/merge/test.yml index 8183a11688c..fca66447718 100644 --- a/tests/modules/stringtie/merge/test.yml +++ b/tests/modules/stringtie/merge/test.yml @@ -5,7 +5,7 @@ - stringtie/merge files: - path: output/stringtie/stringtie.merged.gtf - md5sum: 9fab7049ef2eafdea246fc787d1def40 + md5sum: d959eb2fab0db48ded7275e0a2e83c05 - path: output/stringtie/test.ballgown/e2t.ctab md5sum: 9ae42e056c955a88a883e5e917840d77 - path: output/stringtie/test.ballgown/e_data.ctab @@ -18,9 +18,9 @@ md5sum: 92a98902784e7406ffe054d2adbabc7c - path: output/stringtie/test.coverage.gtf - path: output/stringtie/test.gene.abundance.txt - md5sum: 9708811bcefe0f6384293d6f419f3250 + md5sum: 8bcd8e2730ed3337e2730186dbc184f3 - path: output/stringtie/test.transcripts.gtf - md5sum: 0e42709bfe30c2c7f2574ba664f5fa9f + md5sum: a914bd55b68a4b5f607738b17861e362 - name: stringtie merge test_stringtie_reverse_merge command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config @@ -29,7 +29,7 @@ - stringtie/merge files: - path: output/stringtie/stringtie.merged.gtf - md5sum: afc461bb3cbc368f268a7a45c1b54497 + md5sum: 6da479298d73d5b3216d4e1576a2bdf4 - path: output/stringtie/test.ballgown/e2t.ctab md5sum: 9ae42e056c955a88a883e5e917840d77 - path: output/stringtie/test.ballgown/e_data.ctab @@ -42,6 +42,6 @@ md5sum: 92a98902784e7406ffe054d2adbabc7c - path: output/stringtie/test.coverage.gtf - path: output/stringtie/test.gene.abundance.txt - md5sum: 94b85145d60ab1b80a7f0f6cf08418b0 + md5sum: f289f41b3ba1b9f0aa05d14408f1a5da - path: output/stringtie/test.transcripts.gtf - md5sum: 3196e3d50fd461aae6408e0a70acae68 + md5sum: 9dcdc9577c0fdbb25089eda210267546