From 10ca39a86f1b227a5535238d02398fec686eba72 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Wed, 27 Apr 2022 16:03:44 +0200 Subject: [PATCH 1/3] 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 2/3] 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : - 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" input: path fasta From 1b5d3f5ac2ae61ee35dece20a2aeb8018b6438ce Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 27 Apr 2022 19:21:26 +0100 Subject: [PATCH 3/3] Bump STAR version to 2.7.10a for RSEM modules (#1573) * Bump STAR version to 2.7.10a for RSEM modules * Fix tests --- modules/rsem/calculateexpression/main.nf | 6 +++--- modules/rsem/preparereference/main.nf | 6 +++--- tests/config/test_data.config | 4 ++-- tests/modules/rsem/calculateexpression/test.yml | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/modules/rsem/calculateexpression/main.nf b/modules/rsem/calculateexpression/main.nf index cf147a63..1ab3a635 100644 --- a/modules/rsem/calculateexpression/main.nf +++ b/modules/rsem/calculateexpression/main.nf @@ -2,10 +2,10 @@ process RSEM_CALCULATEEXPRESSION { tag "$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