From 44e13ae439e0788db8afb227e2801815c459982a Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 10 May 2022 21:31:43 +0000 Subject: [PATCH 1/7] add module for snippy --- modules/snippy/run/main.nf | 55 ++++++++++++ modules/snippy/run/meta.yml | 110 +++++++++++++++++++++++ tests/config/pytest_modules.yml | 12 ++- tests/modules/snippy/run/main.nf | 16 ++++ tests/modules/snippy/run/nextflow.config | 5 ++ tests/modules/snippy/run/test.yml | 39 ++++++++ 6 files changed, 233 insertions(+), 4 deletions(-) create mode 100644 modules/snippy/run/main.nf create mode 100644 modules/snippy/run/meta.yml create mode 100644 tests/modules/snippy/run/main.nf create mode 100644 tests/modules/snippy/run/nextflow.config create mode 100644 tests/modules/snippy/run/test.yml diff --git a/modules/snippy/run/main.nf b/modules/snippy/run/main.nf new file mode 100644 index 00000000..73c4b94d --- /dev/null +++ b/modules/snippy/run/main.nf @@ -0,0 +1,55 @@ +process SNIPPY_RUN { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2 ': + 'quay.io/biocontainers/snippy:4.6.0--hdfd78af_2' }" + + input: + tuple val(meta), path(reads) + path reference + + output: + tuple val(meta), path("${prefix}/${prefix}.tab") , emit: tab + tuple val(meta), path("${prefix}/${prefix}.csv") , emit: csv + tuple val(meta), path("${prefix}/${prefix}.html") , emit: html + tuple val(meta), path("${prefix}/${prefix}.vcf") , emit: vcf + tuple val(meta), path("${prefix}/${prefix}.bed") , emit: bed + tuple val(meta), path("${prefix}/${prefix}.gff") , emit: gff + tuple val(meta), path("${prefix}/${prefix}.bam") , emit: bam + tuple val(meta), path("${prefix}/${prefix}.bam.bai") , emit: bai + tuple val(meta), path("${prefix}/${prefix}.log") , emit: log + tuple val(meta), path("${prefix}/${prefix}.aligned.fa") , emit: aligned_fa + tuple val(meta), path("${prefix}/${prefix}.consensus.fa") , emit: consensus_fa + tuple val(meta), path("${prefix}/${prefix}.consensus.subs.fa"), emit: consensus_subs_fa + tuple val(meta), path("${prefix}/${prefix}.raw.vcf") , emit: raw_vcf + tuple val(meta), path("${prefix}/${prefix}.filt.vcf") , emit: filt_vcf + tuple val(meta), path("${prefix}/${prefix}.vcf.gz") , emit: vcf_gz + tuple val(meta), path("${prefix}/${prefix}.vcf.gz.csi") , emit: vcf_csi + tuple val(meta), path("${prefix}/${prefix}.txt") , emit: txt + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def read_inputs = meta.single_end ? "--se ${reads[0]}" : "--R1 ${reads[0]} --R2 ${reads[1]}" + """ + snippy \\ + $args \\ + --cpus $task.cpus \\ + --outdir $prefix \\ + --reference $reference \\ + --prefix $prefix \\ + $read_inputs + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + snippy: \$(echo \$(snippy --version 2>&1) | sed 's/snippy //') + END_VERSIONS + """ +} diff --git a/modules/snippy/run/meta.yml b/modules/snippy/run/meta.yml new file mode 100644 index 00000000..fa176399 --- /dev/null +++ b/modules/snippy/run/meta.yml @@ -0,0 +1,110 @@ +name: snippy +description: Rapid haploid variant calling +keywords: + - variant + - fastq + - bacteria +tools: + - snippy: + description: "Rapid bacterial SNP calling and core genome alignments" + homepage: "https://github.com/tseemann/snippy" + documentation: "https://github.com/tseemann/snippy" + tool_dev_url: "https://github.com/tseemann/snippy" + doi: "" + licence: "['GPL v2']" +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - index: + type: file + description: Reference genome in GenBank (preferred) or FASTA format + pattern: "*.{gbk,gbk.gz,fa,fa.gz}" +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" + - tab: + type: file + description: A simple tab-separated summary of all the variants + pattern: "*.tab" + - csv: + type: file + description: A comma-separated version of the .tab file + pattern: "*.csv" + - html: + type: file + description: A HTML version of the .tab file + pattern: "*.html" + - vcf: + type: file + description: The final annotated variants in VCF format + pattern: "*.vcf" + - bed: + type: file + description: The variants in BED format + pattern: "*.bed" + - gff: + type: file + description: The variants in GFF3 format + pattern: "*.gff" + - bam: + type: file + description: The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates. + pattern: "*.bam" + - bai: + type: file + description: Index for the .bam file + pattern: "*.bam.bai" + - log: + type: file + description: A log file with the commands run and their outputs + pattern: "*.log" + - aligned_fa: + type: file + description: A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants) + pattern: "*.aligned.fa" + - consensus_fa: + type: file + description: A version of the reference genome with all variants instantiated + pattern: "*.consensus.fa" + - consensus_subs_fa: + type: file + description: A version of the reference genome with only substitution variants instantiated + pattern: "*.consensus.subs.fa" + - raw_vcf: + type: file + description: The unfiltered variant calls from Freebayes + pattern: "*.raw.vcf" + - filt_vcf: + type: file + description: The filtered variant calls from Freebayes + pattern: "*.filt.vcf" + - vcf_gz: + type: file + description: Compressed .vcf file via BGZIP + pattern: "*.vcf.gz" + - vcf_csi: + type: file + description: Index for the .vcf.gz via bcftools index + pattern: "*.vcf.gz.csi" + - txt: + type: file + description: Tab-separated columnar list of statistics + pattern: "*.txt" +authors: + - "@rpetit3" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 9afe83fd..5a204ac4 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1643,14 +1643,14 @@ samtools/bam2fq: - modules/samtools/bam2fq/** - tests/modules/samtools/bam2fq/** -samtools/convert: - - modules/samtools/convert/** - - tests/modules/samtools/convert/** - samtools/collatefastq: - modules/samtools/collatefastq/** - tests/modules/samtools/collatefastq/** +samtools/convert: + - modules/samtools/convert/** + - tests/modules/samtools/convert/** + samtools/depth: - modules/samtools/depth/** - tests/modules/samtools/depth/** @@ -1787,6 +1787,10 @@ snapaligner/index: - modules/snapaligner/index/** - tests/modules/snapaligner/index/** +snippy/run: + - modules/snippy/run/** + - tests/modules/snippy/run/** + snpdists: - modules/snpdists/** - tests/modules/snpdists/** diff --git a/tests/modules/snippy/run/main.nf b/tests/modules/snippy/run/main.nf new file mode 100644 index 00000000..bfc4082e --- /dev/null +++ b/tests/modules/snippy/run/main.nf @@ -0,0 +1,16 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SNIPPY_RUN } from '../../../../modules/snippy/run/main.nf' + +workflow test_snippy_run { + + input = [ [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + reference = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + + SNIPPY_RUN ( input, reference ) +} diff --git a/tests/modules/snippy/run/nextflow.config b/tests/modules/snippy/run/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/snippy/run/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/snippy/run/test.yml b/tests/modules/snippy/run/test.yml new file mode 100644 index 00000000..e38e8b9e --- /dev/null +++ b/tests/modules/snippy/run/test.yml @@ -0,0 +1,39 @@ +- name: snippy run test_snippy_run + command: nextflow run tests/modules/snippy/run -entry test_snippy_run -c tests/config/nextflow.config -c tests/modules/snippy/run/nextflow.config + tags: + - snippy + - snippy/run + files: + - path: output/snippy/test/test.aligned.fa + md5sum: 47e3390d4167edf1955d162d37aca5e3 + - path: output/snippy/test/test.bam + - path: output/snippy/test/test.bam.bai + - path: output/snippy/test/test.bed + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/snippy/test/test.consensus.fa + md5sum: 483f4a5dfe60171c86ee9b7e6dff908b + - path: output/snippy/test/test.consensus.subs.fa + md5sum: 483f4a5dfe60171c86ee9b7e6dff908b + - path: output/snippy/test/test.csv + md5sum: 322f942115e5945c2041a88246166703 + - path: output/snippy/test/test.filt.vcf + contains: ['fileformat', 'freebayes', 'CHROM'] + - path: output/snippy/test/test.gff + md5sum: df19e1b84ba6f691d20c72b397c88abf + - path: output/snippy/test/test.html + md5sum: 1ccbf0ffcadae1a6b2e11681d24c9938 + - path: output/snippy/test/test.log + contains: ['snippy', 'consensus', 'subs'] + - path: output/snippy/test/test.raw.vcf + contains: ['fileformat', 'freebayes', 'CHROM'] + - path: output/snippy/test/test.tab + md5sum: beb9bde3bce985e53e8feba9ec5b136e + - path: output/snippy/test/test.txt + contains: ['DateTime', 'ReadFiles', 'VariantTotal'] + - path: output/snippy/test/test.vcf + contains: ['fileformat', 'freebayes', 'CHROM'] + - path: output/snippy/test/test.vcf.gz + - path: output/snippy/test/test.vcf.gz.csi + md5sum: bed9fa291c220a1ba04eb2d448932ffc + - path: output/snippy/versions.yml + md5sum: 518aad56c4dbefb6cbcde5ab38cf7b5d From f15848d4774f095f43594516769fde889a7a3d12 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 10 May 2022 21:44:40 +0000 Subject: [PATCH 2/7] fix typo --- modules/snippy/run/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/snippy/run/meta.yml b/modules/snippy/run/meta.yml index fa176399..13c923d8 100644 --- a/modules/snippy/run/meta.yml +++ b/modules/snippy/run/meta.yml @@ -100,7 +100,7 @@ output: pattern: "*.vcf.gz" - vcf_csi: type: file - description: Index for the .vcf.gz via bcftools index + description: Index for the .vcf.gz via bcftools index pattern: "*.vcf.gz.csi" - txt: type: file From 56e94f625e69e48de7c218b79857cc3a59cb9220 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 10 May 2022 21:47:11 +0000 Subject: [PATCH 3/7] remove empty file md5 --- tests/modules/snippy/run/test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/modules/snippy/run/test.yml b/tests/modules/snippy/run/test.yml index e38e8b9e..ac945e88 100644 --- a/tests/modules/snippy/run/test.yml +++ b/tests/modules/snippy/run/test.yml @@ -9,7 +9,6 @@ - path: output/snippy/test/test.bam - path: output/snippy/test/test.bam.bai - path: output/snippy/test/test.bed - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: output/snippy/test/test.consensus.fa md5sum: 483f4a5dfe60171c86ee9b7e6dff908b - path: output/snippy/test/test.consensus.subs.fa From ef2996e4a5f4f74b4b49bbbd308c3142de8d894d Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 10 May 2022 21:47:57 +0000 Subject: [PATCH 4/7] match names in meta and main --- modules/snippy/run/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/snippy/run/meta.yml b/modules/snippy/run/meta.yml index 13c923d8..2eb008a1 100644 --- a/modules/snippy/run/meta.yml +++ b/modules/snippy/run/meta.yml @@ -1,4 +1,4 @@ -name: snippy +name: snippy_run description: Rapid haploid variant calling keywords: - variant From 7ced6e20de5a69a25fb57b00244a49329709186a Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 11 May 2022 18:00:36 +0000 Subject: [PATCH 5/7] make prettier --- tests/modules/snippy/run/test.yml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/tests/modules/snippy/run/test.yml b/tests/modules/snippy/run/test.yml index ac945e88..10e24f55 100644 --- a/tests/modules/snippy/run/test.yml +++ b/tests/modules/snippy/run/test.yml @@ -1,8 +1,9 @@ - name: snippy run test_snippy_run - command: nextflow run tests/modules/snippy/run -entry test_snippy_run -c tests/config/nextflow.config -c tests/modules/snippy/run/nextflow.config + command: | + nextflow run tests/modules/snippy/run -entry test_snippy_run -c tests/config/nextflow.config -c tests/modules/snippy/run/nextflow.config tags: - - snippy - snippy/run + - snippy files: - path: output/snippy/test/test.aligned.fa md5sum: 47e3390d4167edf1955d162d37aca5e3 @@ -16,21 +17,21 @@ - path: output/snippy/test/test.csv md5sum: 322f942115e5945c2041a88246166703 - path: output/snippy/test/test.filt.vcf - contains: ['fileformat', 'freebayes', 'CHROM'] + contains: ["fileformat", "freebayes", "CHROM"] - path: output/snippy/test/test.gff md5sum: df19e1b84ba6f691d20c72b397c88abf - path: output/snippy/test/test.html md5sum: 1ccbf0ffcadae1a6b2e11681d24c9938 - path: output/snippy/test/test.log - contains: ['snippy', 'consensus', 'subs'] + contains: ["snippy", "consensus", "subs"] - path: output/snippy/test/test.raw.vcf - contains: ['fileformat', 'freebayes', 'CHROM'] + contains: ["fileformat", "freebayes", "CHROM"] - path: output/snippy/test/test.tab md5sum: beb9bde3bce985e53e8feba9ec5b136e - path: output/snippy/test/test.txt - contains: ['DateTime', 'ReadFiles', 'VariantTotal'] + contains: ["DateTime", "ReadFiles", "VariantTotal"] - path: output/snippy/test/test.vcf - contains: ['fileformat', 'freebayes', 'CHROM'] + contains: ["fileformat", "freebayes", "CHROM"] - path: output/snippy/test/test.vcf.gz - path: output/snippy/test/test.vcf.gz.csi md5sum: bed9fa291c220a1ba04eb2d448932ffc From 63db63757cab03cfa7a02c0d0f134b66fbfadea6 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Mon, 30 May 2022 10:15:40 +0200 Subject: [PATCH 6/7] bump picard versions --- modules/picard/addorreplacereadgroups/main.nf | 6 +++--- modules/picard/cleansam/main.nf | 6 +++--- modules/picard/collecthsmetrics/main.nf | 6 +++--- modules/picard/collectmultiplemetrics/main.nf | 6 +++--- modules/picard/collectwgsmetrics/main.nf | 6 +++--- modules/picard/createsequencedictionary/main.nf | 6 +++--- modules/picard/crosscheckfingerprints/main.nf | 6 +++--- modules/picard/filtersamreads/main.nf | 6 +++--- modules/picard/fixmateinformation/main.nf | 6 +++--- modules/picard/liftovervcf/main.nf | 6 +++--- modules/picard/markduplicates/main.nf | 6 +++--- modules/picard/mergesamfiles/main.nf | 6 +++--- modules/picard/sortsam/main.nf | 6 +++--- modules/picard/sortvcf/main.nf | 6 +++--- 14 files changed, 42 insertions(+), 42 deletions(-) diff --git a/modules/picard/addorreplacereadgroups/main.nf b/modules/picard/addorreplacereadgroups/main.nf index fd102f67..aff83c9f 100644 --- a/modules/picard/addorreplacereadgroups/main.nf +++ b/modules/picard/addorreplacereadgroups/main.nf @@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/cleansam/main.nf b/modules/picard/cleansam/main.nf index 62989565..0042c3f1 100644 --- a/modules/picard/cleansam/main.nf +++ b/modules/picard/cleansam/main.nf @@ -2,10 +2,10 @@ process PICARD_CLEANSAM { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf index 06b6b8f3..52d5c84a 100644 --- a/modules/picard/collecthsmetrics/main.nf +++ b/modules/picard/collecthsmetrics/main.nf @@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf index 3c3152df..6fe9881b 100644 --- a/modules/picard/collectmultiplemetrics/main.nf +++ b/modules/picard/collectmultiplemetrics/main.nf @@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf index cab1fe0c..e231afe2 100644 --- a/modules/picard/collectwgsmetrics/main.nf +++ b/modules/picard/collectwgsmetrics/main.nf @@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/createsequencedictionary/main.nf b/modules/picard/createsequencedictionary/main.nf index 2348c496..16a5ff19 100644 --- a/modules/picard/createsequencedictionary/main.nf +++ b/modules/picard/createsequencedictionary/main.nf @@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/picard/crosscheckfingerprints/main.nf b/modules/picard/crosscheckfingerprints/main.nf index d3b59402..c7c4766c 100644 --- a/modules/picard/crosscheckfingerprints/main.nf +++ b/modules/picard/crosscheckfingerprints/main.nf @@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(input1) diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf index adedcdc2..e17c4686 100644 --- a/modules/picard/filtersamreads/main.nf +++ b/modules/picard/filtersamreads/main.nf @@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam), path(readlist) diff --git a/modules/picard/fixmateinformation/main.nf b/modules/picard/fixmateinformation/main.nf index 539b1082..616acce8 100644 --- a/modules/picard/fixmateinformation/main.nf +++ b/modules/picard/fixmateinformation/main.nf @@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/liftovervcf/main.nf b/modules/picard/liftovervcf/main.nf index c92abfeb..a82f1466 100644 --- a/modules/picard/liftovervcf/main.nf +++ b/modules/picard/liftovervcf/main.nf @@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf index 1565c647..87f913d4 100644 --- a/modules/picard/markduplicates/main.nf +++ b/modules/picard/markduplicates/main.nf @@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf index 1e32c63a..d65f518c 100644 --- a/modules/picard/mergesamfiles/main.nf +++ b/modules/picard/mergesamfiles/main.nf @@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bams) diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf index cee60fd1..5e09d907 100644 --- a/modules/picard/sortsam/main.nf +++ b/modules/picard/sortsam/main.nf @@ -2,10 +2,10 @@ process PICARD_SORTSAM { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/sortvcf/main.nf b/modules/picard/sortvcf/main.nf index fb8dbb79..8f886393 100644 --- a/modules/picard/sortvcf/main.nf +++ b/modules/picard/sortvcf/main.nf @@ -2,10 +2,10 @@ process PICARD_SORTVCF { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(vcf) From d7cec801b244d8aa0a98aa94934b191ed5720f92 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Fri, 3 Jun 2022 13:05:43 -0600 Subject: [PATCH 7/7] Update main.nf --- modules/snippy/run/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/snippy/run/main.nf b/modules/snippy/run/main.nf index 73c4b94d..5ecdbea8 100644 --- a/modules/snippy/run/main.nf +++ b/modules/snippy/run/main.nf @@ -4,7 +4,7 @@ process SNIPPY_RUN { conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2 ': + 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2' : 'quay.io/biocontainers/snippy:4.6.0--hdfd78af_2' }" input: