From 9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 22 Apr 2022 14:50:07 +0100 Subject: [PATCH 01/13] Replace vanilla Linux Biocontainer with Ubuntu (#1557) --- modules/cat/fastq/main.nf | 4 ++-- modules/gunzip/main.nf | 4 ++-- modules/untar/main.nf | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/modules/cat/fastq/main.nf b/modules/cat/fastq/main.nf index bf0877c3..b6854895 100644 --- a/modules/cat/fastq/main.nf +++ b/modules/cat/fastq/main.nf @@ -4,8 +4,8 @@ process CAT_FASTQ { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : - 'biocontainers/biocontainers:v1.2.0_cv1' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/gunzip/main.nf b/modules/gunzip/main.nf index 9d4b0666..61bf1afa 100644 --- a/modules/gunzip/main.nf +++ b/modules/gunzip/main.nf @@ -4,8 +4,8 @@ process GUNZIP { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : - 'biocontainers/biocontainers:v1.2.0_cv1' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(archive) diff --git a/modules/untar/main.nf b/modules/untar/main.nf index bbfa0bfe..058d1764 100644 --- a/modules/untar/main.nf +++ b/modules/untar/main.nf @@ -2,10 +2,10 @@ process UNTAR { tag "$archive" label 'process_low' - conda (params.enable_conda ? "conda-forge::tar=1.34" : null) + conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' : - 'biocontainers/biocontainers:v1.2.0_cv2' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(archive) From 6d88f2da8cc5d586456e801b535cc4213e0fa2f7 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 22 Apr 2022 15:13:06 +0100 Subject: [PATCH 02/13] Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Rename process from STRINGTIE to STRINGTIE_STRINGTIE * Bump Stringtie version to 2.2.1 and remove empty files in tests * Fix tests for stringtie/merge Co-authored-by: Júlia Mir Pedrol --- modules/stringtie/merge/main.nf | 6 +++--- modules/stringtie/stringtie/main.nf | 8 ++++---- modules/stringtie/stringtie/meta.yml | 2 +- tests/modules/stringtie/merge/main.nf | 12 ++++++------ tests/modules/stringtie/merge/test.yml | 14 ++++++-------- tests/modules/stringtie/stringtie/main.nf | 6 +++--- tests/modules/stringtie/stringtie/test.yml | 2 -- 7 files changed, 23 insertions(+), 27 deletions(-) diff --git a/modules/stringtie/merge/main.nf b/modules/stringtie/merge/main.nf index aa11eb36..c8460c94 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' : - 'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }" + 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : + 'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }" input: path stringtie_gtf diff --git a/modules/stringtie/stringtie/main.nf b/modules/stringtie/stringtie/main.nf index f37e347a..c70c9819 100644 --- a/modules/stringtie/stringtie/main.nf +++ b/modules/stringtie/stringtie/main.nf @@ -1,11 +1,11 @@ -process STRINGTIE { +process STRINGTIE_STRINGTIE { tag "$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 a462c574..0dda84d0 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/main.nf b/tests/modules/stringtie/merge/main.nf index 7851e755..3fe32902 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 392a1d7c..fca66447 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 @@ -17,11 +17,10 @@ - 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 + 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 @@ -30,7 +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 @@ -42,8 +41,7 @@ - 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 + md5sum: f289f41b3ba1b9f0aa05d14408f1a5da - path: output/stringtie/test.transcripts.gtf - md5sum: 3196e3d50fd461aae6408e0a70acae68 + md5sum: 9dcdc9577c0fdbb25089eda210267546 diff --git a/tests/modules/stringtie/stringtie/main.nf b/tests/modules/stringtie/stringtie/main.nf index ae6abe67..463e4b98 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 ) } diff --git a/tests/modules/stringtie/stringtie/test.yml b/tests/modules/stringtie/stringtie/test.yml index 732b9fd1..2815ba81 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 b3e56c83c683111d0d3edfa2821454d6132b6b66 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Fri, 22 Apr 2022 16:29:49 +0200 Subject: [PATCH 03/13] Remove task.cpus from the command (#1559) --- modules/phantompeakqualtools/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/phantompeakqualtools/main.nf b/modules/phantompeakqualtools/main.nf index f584cb65..0362b2e7 100644 --- a/modules/phantompeakqualtools/main.nf +++ b/modules/phantompeakqualtools/main.nf @@ -26,7 +26,7 @@ process PHANTOMPEAKQUALTOOLS { def prefix = task.ext.prefix ?: "${meta.id}" """ RUN_SPP=`which run_spp.R` - Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus + Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" cat <<-END_VERSIONS > versions.yml "${task.process}": From 99576895682ee210065be35596b28f308aba068d Mon Sep 17 00:00:00 2001 From: Jasmin F <73216762+jasmezz@users.noreply.github.com> Date: Fri, 22 Apr 2022 17:51:18 +0200 Subject: [PATCH 04/13] Add missing bacteroides_fragilis genome.gbff.gz (#1558) Co-authored-by: James A. Fellows Yates --- tests/config/test_data.config | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 559c0d6f..f6ea242d 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -335,6 +335,7 @@ params { 'bacteroides_fragilis' { 'genome' { genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" + genome_gbff_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz" genome_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf" genome_mapping_potential_arg = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG" From 378fa5fbb47ed7c8211b01acb5cf1f66111c4e13 Mon Sep 17 00:00:00 2001 From: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Date: Sat, 23 Apr 2022 10:12:06 -0400 Subject: [PATCH 05/13] new module: GAMMA (#1532) * initial version of gamma module * remove trailing whitespace * prettier fix * hardcode version number * Update modules/gamma/main.nf Co-authored-by: James A. Fellows Yates * Update modules/gamma/main.nf Co-authored-by: James A. Fellows Yates * Update modules/gamma/meta.yml Co-authored-by: Robert A. Petit III * update meta and prettier * add whitespaces * add fasta output and tests Co-authored-by: Robert A. Petit III Co-authored-by: James A. Fellows Yates --- modules/gamma/main.nf | 41 +++++++++++++++++++ modules/gamma/meta.yml | 63 +++++++++++++++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/modules/gamma/main.nf | 17 ++++++++ tests/modules/gamma/nextflow.config | 7 ++++ tests/modules/gamma/test.yml | 13 ++++++ 6 files changed, 145 insertions(+) create mode 100644 modules/gamma/main.nf create mode 100644 modules/gamma/meta.yml create mode 100644 tests/modules/gamma/main.nf create mode 100644 tests/modules/gamma/nextflow.config create mode 100644 tests/modules/gamma/test.yml diff --git a/modules/gamma/main.nf b/modules/gamma/main.nf new file mode 100644 index 00000000..e176ee68 --- /dev/null +++ b/modules/gamma/main.nf @@ -0,0 +1,41 @@ +def VERSION = '2.1' // Version information not provided by tool on CLI + +process GAMMA { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::gamma=2.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0': + 'quay.io/biocontainers/gamma:2.1--hdfd78af_0' }" + + input: + tuple val(meta), path(fasta) + path(db) + + output: + tuple val(meta), path("*.gamma") , emit: gamma + tuple val(meta), path("*.psl") , emit: psl + tuple val(meta), path("*.gff") , optional:true , emit: gff + tuple val(meta), path("*.fasta"), optional:true , emit: fasta + 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}" + """ + GAMMA.py \\ + $args \\ + $fasta \\ + $db \\ + $prefix + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gamma: $VERSION + END_VERSIONS + """ +} diff --git a/modules/gamma/meta.yml b/modules/gamma/meta.yml new file mode 100644 index 00000000..316b685b --- /dev/null +++ b/modules/gamma/meta.yml @@ -0,0 +1,63 @@ +name: "gamma" +description: Gene Allele Mutation Microbial Assessment +keywords: + - gamma + - gene-calling +tools: + - "gamma": + description: "Tool for Gene Allele Mutation Microbial Assessment" + homepage: "https://github.com/rastanton/GAMMA" + documentation: "https://github.com/rastanton/GAMMA" + tool_dev_url: "https://github.com/rastanton/GAMMA" + doi: "10.1093/bioinformatics/btab607" + licence: "['Apache License 2.0']" + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" + - db: + type: file + description: Database in FASTA format + pattern: "*.{fa,fasta}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + + - gamma: + type: file + description: GAMMA file with annotated gene matches + pattern: "*.{gamma}" + + - psl: + type: file + description: PSL file with all gene matches found + pattern: "*.{psl}" + + - gff: + type: file + description: GFF file + pattern: "*.{gff}" + + - fasta: + type: file + description: multifasta file of the gene matches + pattern: "*.{fasta}" + +authors: + - "@sateeshperi" + - "@rastanton" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index a1a969e7..263e83a8 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -675,6 +675,10 @@ freebayes: - modules/freebayes/** - tests/modules/freebayes/** +gamma: + - modules/gamma/** + - tests/modules/gamma/** + gatk4/applybqsr: - modules/gatk4/applybqsr/** - tests/modules/gatk4/applybqsr/** diff --git a/tests/modules/gamma/main.nf b/tests/modules/gamma/main.nf new file mode 100644 index 00000000..f9477706 --- /dev/null +++ b/tests/modules/gamma/main.nf @@ -0,0 +1,17 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GAMMA } from '../../../modules/gamma/main.nf' + +workflow test_gamma { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + + db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ] + + GAMMA ( input, db ) +} diff --git a/tests/modules/gamma/nextflow.config b/tests/modules/gamma/nextflow.config new file mode 100644 index 00000000..bbbf4de0 --- /dev/null +++ b/tests/modules/gamma/nextflow.config @@ -0,0 +1,7 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + ext.args = '--fasta' + +} diff --git a/tests/modules/gamma/test.yml b/tests/modules/gamma/test.yml new file mode 100644 index 00000000..1b493b49 --- /dev/null +++ b/tests/modules/gamma/test.yml @@ -0,0 +1,13 @@ +- name: gamma test_gamma + command: nextflow run tests/modules/gamma -entry test_gamma -c tests/config/nextflow.config + tags: + - gamma + files: + - path: output/gamma/test.fasta + md5sum: df37b48466181311e0a679f3c5878484 + - path: output/gamma/test.gamma + md5sum: 3256708fa517a65ed01d99e0e3c762ae + - path: output/gamma/test.psl + md5sum: 162a2757ed3b167ae1e0cdb24213f940 + - path: output/gamma/versions.yml + md5sum: 3fefb5b46c94993362243c5f9a472057 From 569e07f0af74e2a6ea43fca61ae90bb762893461 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 25 Apr 2022 14:32:49 +0200 Subject: [PATCH 06/13] add samtools/bamtocram modules (#1561) * add new samtools/bamtocram module * fix md5sum * remove md5sum * Update modules/samtools/bamtocram/main.nf Co-authored-by: James A. Fellows Yates Co-authored-by: James A. Fellows Yates --- modules/samtools/bamtocram/main.nf | 35 +++++++++++++ modules/samtools/bamtocram/meta.yml | 52 +++++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/modules/samtools/bamtocram/main.nf | 17 ++++++ .../samtools/bamtocram/nextflow.config | 5 ++ tests/modules/samtools/bamtocram/test.yml | 9 ++++ 6 files changed, 122 insertions(+) create mode 100644 modules/samtools/bamtocram/main.nf create mode 100644 modules/samtools/bamtocram/meta.yml create mode 100644 tests/modules/samtools/bamtocram/main.nf create mode 100644 tests/modules/samtools/bamtocram/nextflow.config create mode 100644 tests/modules/samtools/bamtocram/test.yml diff --git a/modules/samtools/bamtocram/main.nf b/modules/samtools/bamtocram/main.nf new file mode 100644 index 00000000..b49c308f --- /dev/null +++ b/modules/samtools/bamtocram/main.nf @@ -0,0 +1,35 @@ +//There is a -L option to only output alignments in interval, might be an option for exons/panel data? +process SAMTOOLS_BAMTOCRAM { + tag "$meta.id" + label 'process_medium' + + conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + + input: + tuple val(meta), path(input), path(index) + path fasta + path fai + + output: + tuple val(meta), path("*.cram"), path("*.crai"), emit: cram_crai + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + samtools view --threads ${task.cpus} --reference ${fasta} -C $args $input > ${prefix}.cram + samtools index -@${task.cpus} ${prefix}.cram + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/samtools/bamtocram/meta.yml b/modules/samtools/bamtocram/meta.yml new file mode 100644 index 00000000..037704c6 --- /dev/null +++ b/modules/samtools/bamtocram/meta.yml @@ -0,0 +1,52 @@ +name: samtools_bamtocram +description: filter/convert and then index CRAM file +keywords: + - view + - index + - bam + - cram +tools: + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/SAM file + pattern: "*.{bam,sam}" + - index: + type: file + description: BAM/SAM index file + pattern: "*.{bai,sai}" + - fasta: + type: file + description: Reference file to create the CRAM file + pattern: "*.{fasta,fa}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cram_crai: + type: file + description: filtered/converted CRAM file + index + pattern: "*{.cram,.crai}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@FriederikeHanssen" + - "@maxulysse" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 263e83a8..4d8ce0b5 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1595,6 +1595,10 @@ samtools/bam2fq: - modules/samtools/bam2fq/** - tests/modules/samtools/bam2fq/** +samtools/bamtocram: + - modules/samtools/bamtocram/** + - tests/modules/samtools/bamtocram/** + samtools/collatefastq: - modules/samtools/collatefastq/** - tests/modules/samtools/collatefastq/** diff --git a/tests/modules/samtools/bamtocram/main.nf b/tests/modules/samtools/bamtocram/main.nf new file mode 100644 index 00000000..b1743310 --- /dev/null +++ b/tests/modules/samtools/bamtocram/main.nf @@ -0,0 +1,17 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/bamtocram/main.nf' + +workflow test_samtools_bamtocram { + + input = [ [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)] + + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + + SAMTOOLS_BAMTOCRAM ( input, fasta, fai ) +} \ No newline at end of file diff --git a/tests/modules/samtools/bamtocram/nextflow.config b/tests/modules/samtools/bamtocram/nextflow.config new file mode 100644 index 00000000..8730f1c4 --- /dev/null +++ b/tests/modules/samtools/bamtocram/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} diff --git a/tests/modules/samtools/bamtocram/test.yml b/tests/modules/samtools/bamtocram/test.yml new file mode 100644 index 00000000..3cb82902 --- /dev/null +++ b/tests/modules/samtools/bamtocram/test.yml @@ -0,0 +1,9 @@ +- name: samtools bamtocram test_samtools_bamtocram + command: nextflow run ./tests/modules/samtools/bamtocram -entry test_samtools_bamtocram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bamtocram/nextflow.config + tags: + - samtools/bamtocram + - samtools + files: + - path: output/samtools/test.cram + - path: output/samtools/test.cram.crai + - path: output/samtools/versions.yml From 6a46e7cf117bbae41bca9b4c7ff7a77794df16ec Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Mon, 25 Apr 2022 19:07:43 +0200 Subject: [PATCH 07/13] Allow to pass arguments to the phantompeakqualtools script itself (#1562) * Allow to pass arguments to the script itself * Place args2 correctly * Define args2 aaaaarrrrgggg * Testing locally before commiting is a good practice * Update modules/phantompeakqualtools/main.nf Co-authored-by: Harshil Patel Co-authored-by: Harshil Patel --- modules/phantompeakqualtools/main.nf | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/modules/phantompeakqualtools/main.nf b/modules/phantompeakqualtools/main.nf index 0362b2e7..d8f73342 100644 --- a/modules/phantompeakqualtools/main.nf +++ b/modules/phantompeakqualtools/main.nf @@ -22,11 +22,12 @@ process PHANTOMPEAKQUALTOOLS { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ RUN_SPP=`which run_spp.R` - Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" + Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" $args2 cat <<-END_VERSIONS > versions.yml "${task.process}": From 1f77bc130b26309573670c58053a928a4602a925 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 26 Apr 2022 16:32:20 +0200 Subject: [PATCH 08/13] Update minimap2/align module (#1537) --- modules/minimap2/align/main.nf | 22 ++++++++++++++++------ modules/minimap2/align/meta.yml | 18 ++++++++++++++++++ tests/modules/minimap2/align/main.nf | 10 ++++++++-- tests/modules/minimap2/align/test.yml | 16 ++++++++-------- 4 files changed, 50 insertions(+), 16 deletions(-) diff --git a/modules/minimap2/align/main.nf b/modules/minimap2/align/main.nf index fe06f14d..7ba05ee9 100644 --- a/modules/minimap2/align/main.nf +++ b/modules/minimap2/align/main.nf @@ -2,18 +2,22 @@ process MINIMAP2_ALIGN { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) + conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' : - 'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' : + 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }" input: tuple val(meta), path(reads) path reference + val bam_format + val cigar_paf_format + val cigar_bam output: - tuple val(meta), path("*.paf"), emit: paf - path "versions.yml" , emit: versions + tuple val(meta), path("*.paf"), optional: true, emit: paf + tuple val(meta), path("*.bam"), optional: true, emit: bam + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -22,13 +26,19 @@ process MINIMAP2_ALIGN { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}" + def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf" + def cigar_paf = cigar_paf_format && !sam_format ? "-c" : '' + def set_cigar_bam = cigar_bam && sam_format ? "-L" : '' """ minimap2 \\ $args \\ -t $task.cpus \\ $reference \\ $input_reads \\ - > ${prefix}.paf + $cigar_paf \\ + $set_cigar_bam \\ + $bam_output + cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/minimap2/align/meta.yml b/modules/minimap2/align/meta.yml index 89e24283..991b39a0 100644 --- a/modules/minimap2/align/meta.yml +++ b/modules/minimap2/align/meta.yml @@ -29,6 +29,17 @@ input: type: file description: | Reference database in FASTA format. + - bam_format: + type: boolean + description: Specify that output should be in BAM format + - cigar_paf_format: + type: boolean + description: Specify that output CIGAR should be in PAF format + - cigar_bam: + type: boolean + description: | + Write CIGAR with >65535 ops at the CG tag. This is recommended when + doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations) output: - meta: type: map @@ -39,9 +50,16 @@ output: type: file description: Alignment in PAF format pattern: "*.paf" + - bam: + type: file + description: Alignment in BAM format + pattern: "*.bam" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@heuermh" + - "@sofstam" + - "@sateeshperi" + - "@jfy133" diff --git a/tests/modules/minimap2/align/main.nf b/tests/modules/minimap2/align/main.nf index e507d3e5..ee6c0838 100644 --- a/tests/modules/minimap2/align/main.nf +++ b/tests/modules/minimap2/align/main.nf @@ -9,8 +9,11 @@ workflow test_minimap2_align_single_end { [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)] ] fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + bam_format = true + cigar_paf_format = false + cigar_bam = false - MINIMAP2_ALIGN ( input, fasta ) + MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam) } workflow test_minimap2_align_paired_end { @@ -19,6 +22,9 @@ workflow test_minimap2_align_paired_end { file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + bam_format = true + cigar_paf_format = false + cigar_bam = false - MINIMAP2_ALIGN ( input, fasta ) + MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam ) } diff --git a/tests/modules/minimap2/align/test.yml b/tests/modules/minimap2/align/test.yml index 73dd73e2..c392e313 100644 --- a/tests/modules/minimap2/align/test.yml +++ b/tests/modules/minimap2/align/test.yml @@ -1,17 +1,17 @@ -- name: minimap2 align single-end - command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config +- name: minimap2 align test_minimap2_align_single_end + command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config tags: - minimap2 - minimap2/align files: - - path: ./output/minimap2/test.paf - md5sum: 70e8cf299ee3ecd33e629d10c1f588ce + - path: output/minimap2/test.bam + - path: output/minimap2/versions.yml -- name: minimap2 align paired-end - command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config +- name: minimap2 align test_minimap2_align_paired_end + command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config tags: - minimap2 - minimap2/align files: - - path: ./output/minimap2/test.paf - md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28 + - path: output/minimap2/test.bam + - path: output/minimap2/versions.yml From 85ec13ff1fc2196c5a507ea497de468101baabed Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 26 Apr 2022 19:15:24 +0100 Subject: [PATCH 09/13] Add Trimgalore output for unpaired reads (#1568) * Add Trimgalore output for unpaired reads * Use glob instead of outprefix --- modules/trimgalore/main.nf | 13 ++++++++----- modules/trimgalore/meta.yml | 5 +++++ 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/modules/trimgalore/main.nf b/modules/trimgalore/main.nf index 9487c799..3a3fca90 100644 --- a/modules/trimgalore/main.nf +++ b/modules/trimgalore/main.nf @@ -11,12 +11,13 @@ process TRIMGALORE { tuple val(meta), path(reads) output: - tuple val(meta), path("*.fq.gz") , emit: reads - tuple val(meta), path("*report.txt"), emit: log - path "versions.yml" , emit: versions + tuple val(meta), path("*{trimmed,val}*.fq.gz"), emit: reads + tuple val(meta), path("*report.txt") , emit: log + path "versions.yml" , emit: versions - tuple val(meta), path("*.html"), emit: html optional true - tuple val(meta), path("*.zip") , emit: zip optional true + tuple val(meta), path("*unpaired*.fq.gz") , emit: unpaired, optional: true + tuple val(meta), path("*.html") , emit: html , optional: true + tuple val(meta), path("*.zip") , emit: zip , optional: true when: task.ext.when == null || task.ext.when @@ -52,6 +53,7 @@ process TRIMGALORE { $c_r1 \\ $tpc_r1 \\ ${prefix}.fastq.gz + cat <<-END_VERSIONS > versions.yml "${task.process}": trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') @@ -73,6 +75,7 @@ process TRIMGALORE { $tpc_r2 \\ ${prefix}_1.fastq.gz \\ ${prefix}_2.fastq.gz + cat <<-END_VERSIONS > versions.yml "${task.process}": trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') diff --git a/modules/trimgalore/meta.yml b/modules/trimgalore/meta.yml index e99a8833..439f566d 100644 --- a/modules/trimgalore/meta.yml +++ b/modules/trimgalore/meta.yml @@ -37,6 +37,11 @@ output: List of input adapter trimmed FastQ files of size 1 and 2 for single-end and paired-end data, respectively. pattern: "*.{fq.gz}" + - unpaired: + type: file + description: | + FastQ files containing unpaired reads from read 1 or read 2 + pattern: "*unpaired*.fq.gz" - html: type: file description: FastQC report (optional) From 61e740f79cbb4538483e751ad82ca71c592f3079 Mon Sep 17 00:00:00 2001 From: Jasmin F <73216762+jasmezz@users.noreply.github.com> Date: Wed, 27 Apr 2022 12:40:04 +0200 Subject: [PATCH 10/13] Add antismash download DB: missing container folders as output channels (#1567) * Add missing container folders as output channels * Apply suggestions from code review Co-authored-by: James A. Fellows Yates * Update tool name * Update test output checksum Co-authored-by: James A. Fellows Yates --- .../antismashlitedownloaddatabases/main.nf | 8 +++++-- .../antismashlitedownloaddatabases/meta.yml | 21 ++++++++++++++++--- .../antismashlitedownloaddatabases/test.yml | 7 +++++-- 3 files changed, 29 insertions(+), 7 deletions(-) diff --git a/modules/antismash/antismashlitedownloaddatabases/main.nf b/modules/antismash/antismashlitedownloaddatabases/main.nf index 1853d80a..72314eee 100644 --- a/modules/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/antismash/antismashlitedownloaddatabases/main.nf @@ -7,8 +7,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { 'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }" /* - These files are normally downloaded by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH. + These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH. Reason: Upon execution, the tool checks if certain database files are present within the container and if not, it tries to create them in /usr/local/bin, for which only root user has write permissions. Mounting those database files with this module prevents the tool from trying to create them. + These files are also emitted as output channels in this module to enable the antismash-lite module to use them as mount volumes to the docker/singularity containers. */ containerOptions { @@ -26,6 +27,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { output: path("antismash_db") , emit: database + path("css"), emit: css_dir + path("detection"), emit: detection_dir + path("modules"), emit: modules_dir path "versions.yml", emit: versions when: @@ -40,7 +44,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { cat <<-END_VERSIONS > versions.yml "${task.process}": - antismash: \$(antismash --version | sed 's/antiSMASH //') + antismash-lite: \$(antismash --version | sed 's/antiSMASH //') END_VERSIONS """ } diff --git a/modules/antismash/antismashlitedownloaddatabases/meta.yml b/modules/antismash/antismashlitedownloaddatabases/meta.yml index ad393bae..619dc8c2 100644 --- a/modules/antismash/antismashlitedownloaddatabases/meta.yml +++ b/modules/antismash/antismashlitedownloaddatabases/meta.yml @@ -27,17 +27,17 @@ input: - database_css: type: directory description: | - antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. + antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. pattern: "css" - database_detection: type: directory description: | - antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. + antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. pattern: "detection" - database_modules: type: directory description: | - antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. + antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. pattern: "modules" output: @@ -50,6 +50,21 @@ output: type: directory description: Download directory for antiSMASH databases pattern: "antismash_db" + - css_dir: + type: directory + description: | + antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. + pattern: "css" + - detection_dir: + type: directory + description: | + antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. + pattern: "detection" + - modules_dir: + type: directory + description: | + antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. + pattern: "modules" authors: - "@jasmezz" diff --git a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml index 3493bb4b..1079363c 100644 --- a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml +++ b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml @@ -1,14 +1,17 @@ - name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config tags: - - antismash/antismashlitedownloaddatabases - antismash + - antismash/antismashlitedownloaddatabases files: - path: output/antismash/versions.yml - md5sum: e2656c8d2bcc7469eba40eb1ee5c91b3 + md5sum: 24859c67023abab99de295d3675a24b6 - path: output/antismash/antismash_db - path: output/antismash/antismash_db/clusterblast - path: output/antismash/antismash_db/clustercompare - path: output/antismash/antismash_db/pfam - path: output/antismash/antismash_db/resfam - path: output/antismash/antismash_db/tigrfam + - path: output/antismash/css + - path: output/antismash/detection + - path: output/antismash/modules From 10ca39a86f1b227a5535238d02398fec686eba72 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Wed, 27 Apr 2022 16:03:44 +0200 Subject: [PATCH 11/13] add intervals possibilities to splitncigarreads (#1571) --- modules/gatk4/splitncigarreads/main.nf | 4 +++- modules/gatk4/splitncigarreads/meta.yml | 7 +++++++ tests/modules/gatk4/splitncigarreads/main.nf | 18 +++++++++++++++++- tests/modules/gatk4/splitncigarreads/test.yml | 11 ++++++++++- 4 files changed, 37 insertions(+), 3 deletions(-) diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf index f7c559d9..85e5daa8 100644 --- a/modules/gatk4/splitncigarreads/main.nf +++ b/modules/gatk4/splitncigarreads/main.nf @@ -8,7 +8,7 @@ process GATK4_SPLITNCIGARREADS { 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: - tuple val(meta), path(bam) + tuple val(meta), path(bam), path(bai), path(intervals) path fasta path fai path dict @@ -23,6 +23,7 @@ process GATK4_SPLITNCIGARREADS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def interval_command = intervals ? "--intervals $intervals" : "" def avail_mem = 3 if (!task.memory) { @@ -35,6 +36,7 @@ process GATK4_SPLITNCIGARREADS { --input $bam \\ --output ${prefix}.bam \\ --reference $fasta \\ + $interval_command \\ --tmp-dir . \\ $args diff --git a/modules/gatk4/splitncigarreads/meta.yml b/modules/gatk4/splitncigarreads/meta.yml index 407e80bd..76bfdcd3 100644 --- a/modules/gatk4/splitncigarreads/meta.yml +++ b/modules/gatk4/splitncigarreads/meta.yml @@ -23,6 +23,13 @@ input: type: list description: BAM/SAM/CRAM file containing reads pattern: "*.{bam,sam,cram}" + - bai: + type: list + description: BAI/SAI/CRAI index file (optional) + pattern: "*.{bai,sai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) - fasta: type: file description: The reference fasta file diff --git a/tests/modules/gatk4/splitncigarreads/main.nf b/tests/modules/gatk4/splitncigarreads/main.nf index 7e5b7c9a..31e45cec 100644 --- a/tests/modules/gatk4/splitncigarreads/main.nf +++ b/tests/modules/gatk4/splitncigarreads/main.nf @@ -6,7 +6,23 @@ include { GATK4_SPLITNCIGARREADS } from '../../../../modules/gatk4/splitncigarre workflow test_gatk4_splitncigarreads { input = [ [ id:'test' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ] + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), + [], + [] + ] + + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + + GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict ) +} + +workflow test_gatk4_splitncigarreads_intervals { + input = [ [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) diff --git a/tests/modules/gatk4/splitncigarreads/test.yml b/tests/modules/gatk4/splitncigarreads/test.yml index c38064e2..d9a58901 100644 --- a/tests/modules/gatk4/splitncigarreads/test.yml +++ b/tests/modules/gatk4/splitncigarreads/test.yml @@ -5,5 +5,14 @@ - gatk4/splitncigarreads files: - path: output/gatk4/test.bam - md5sum: ceed15c0bd64ff5c38d3816905933b0b + md5sum: 436d8e31285c6b588bdd1c7f1d07f6f2 + - path: output/gatk4/versions.yml +- name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals + command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c tests/config/nextflow.config + tags: + - gatk4 + - gatk4/splitncigarreads + files: + - path: output/gatk4/test.bam + md5sum: cd56e3225950f519fd47164cca60a0bb - path: output/gatk4/versions.yml From 213403187932dbbdd936a04474cc8cd8abae7a08 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 27 Apr 2022 18:15:11 +0100 Subject: [PATCH 12/13] Bump SAMtools version for custom/getchromsizes (#1572) --- modules/custom/getchromsizes/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/custom/getchromsizes/main.nf b/modules/custom/getchromsizes/main.nf index bbcfa9be..0eabf3a4 100644 --- a/modules/custom/getchromsizes/main.nf +++ b/modules/custom/getchromsizes/main.nf @@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES { tag "$fasta" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.15" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : - 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" input: path fasta From 1b5d3f5ac2ae61ee35dece20a2aeb8018b6438ce Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 27 Apr 2022 19:21:26 +0100 Subject: [PATCH 13/13] Bump STAR version to 2.7.10a for RSEM modules (#1573) * Bump STAR version to 2.7.10a for RSEM modules * Fix tests --- modules/rsem/calculateexpression/main.nf | 6 +++--- modules/rsem/preparereference/main.nf | 6 +++--- tests/config/test_data.config | 4 ++-- tests/modules/rsem/calculateexpression/test.yml | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/modules/rsem/calculateexpression/main.nf b/modules/rsem/calculateexpression/main.nf index cf147a63..1ab3a635 100644 --- a/modules/rsem/calculateexpression/main.nf +++ b/modules/rsem/calculateexpression/main.nf @@ -2,10 +2,10 @@ process RSEM_CALCULATEEXPRESSION { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null) + conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' : - 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' : + 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }" input: tuple val(meta), path(reads) diff --git a/modules/rsem/preparereference/main.nf b/modules/rsem/preparereference/main.nf index 2d2ca205..da11be45 100644 --- a/modules/rsem/preparereference/main.nf +++ b/modules/rsem/preparereference/main.nf @@ -2,10 +2,10 @@ process RSEM_PREPAREREFERENCE { tag "$fasta" label 'process_high' - conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null) + conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' : - 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' : + 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }" input: path fasta, stageAs: "rsem/*" diff --git a/tests/config/test_data.config b/tests/config/test_data.config index f6ea242d..b3171a51 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -245,8 +245,8 @@ params { test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz" test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz" test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz" - test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_1.fastq.gz" - test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_2.fastq.gz" + test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz" + test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz" test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table" test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table" diff --git a/tests/modules/rsem/calculateexpression/test.yml b/tests/modules/rsem/calculateexpression/test.yml index f19c3398..b0251de9 100644 --- a/tests/modules/rsem/calculateexpression/test.yml +++ b/tests/modules/rsem/calculateexpression/test.yml @@ -42,7 +42,7 @@ - path: output/rsem/rsem/genome.transcripts.fa md5sum: 050c521a2719c2ae48267c1e65218f29 - path: output/rsem/rsem/genomeParameters.txt - md5sum: 2fe3a030e1706c3e8cd4df3818e6dd2f + md5sum: df5a456e3242520cc36e0083a6a7d9dd - path: output/rsem/rsem/sjdbInfo.txt md5sum: 5690ea9d9f09f7ff85b7fd47bd234903 - path: output/rsem/rsem/sjdbList.fromGTF.out.tab @@ -63,4 +63,4 @@ - path: output/rsem/test.stat/test.theta md5sum: de2e4490c98cc5383a86ae8225fd0a28 - path: output/rsem/test.transcript.bam - md5sum: 7846491086c478858419667d60f18edd + md5sum: ed681d39f5700ffc74d6321525330d93