diff --git a/CHANGELOG.md b/CHANGELOG.md index 1ee69f38b..83e2bc3b4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1480](https://github.com/nf-core/rnaseq/pull/1480) - Bump version after release 3.18.0 - [PR #1482](https://github.com/nf-core/rnaseq/pull/1482) - Update trimgalore module for save_unpaired fix +- [pR #1486](https://github.com/nf-core/rnaseq/pull/1486) - Bump STAR build for multiprocessing fix # 3.18.0 - 2024-12-19 diff --git a/conf/arm.config b/conf/arm.config index 275af8c99..881db8748 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -121,11 +121,11 @@ process { } withName: 'STAR_GENOMEGENERATE' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' } + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/40/40d803371e50330de0773c7cc50315e2c3b4b41dcf123823adeb0a07d71654c1/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' } } withName: 'STAR_ALIGN' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' } + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/40/40d803371e50330de0773c7cc50315e2c3b4b41dcf123823adeb0a07d71654c1/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' } } withName: 'TXIMETA_TXIMPORT' { diff --git a/modules.json b/modules.json index 53acd6075..1c8fbb6f6 100644 --- a/modules.json +++ b/modules.json @@ -227,13 +227,13 @@ }, "star/align": { "branch": "master", - "git_sha": "6a367612c2c27aa659293c656afa764361223db4", + "git_sha": "3c259f0ac1ed9ae3f6b835461d054edffc60120e", "installed_by": ["modules"], "patch": "modules/nf-core/star/align/star-align.diff" }, "star/genomegenerate": { "branch": "master", - "git_sha": "6a367612c2c27aa659293c656afa764361223db4", + "git_sha": "3c259f0ac1ed9ae3f6b835461d054edffc60120e", "installed_by": ["modules"], "patch": "modules/nf-core/star/genomegenerate/star-genomegenerate.diff" }, diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index c6b651bdd..16aabaede 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -3,7 +3,7 @@ process STAR_ALIGN { label 'process_high' conda "${moduleDir}/environment.yml" - container 'nf-core/htslib_samtools_star_gawk:311d422a50e6d829' + container 'nf-core/htslib_samtools_star_gawk:ae438e9a604351a4' input: tuple val(meta), path(reads, stageAs: "input*/*") @@ -39,12 +39,13 @@ process STAR_ALIGN { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" - def reads1 = [], reads2 = [] + def reads1 = [] + def reads2 = [] meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v } def ignore_gtf = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf" - def seq_platform = seq_platform ? "'PL:$seq_platform'" : "" - def seq_center = seq_center ? "'CN:$seq_center'" : "" - attrRG = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center 'SM:$prefix' $seq_platform" + def seq_platform_arg = seq_platform ? "'PL:$seq_platform'" : "" + def seq_center_arg = seq_center ? "'CN:$seq_center'" : "" + attrRG = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center_arg 'SM:$prefix' $seq_platform_arg" def out_sam_type = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted' mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : '' """ diff --git a/modules/nf-core/star/align/star-align.diff b/modules/nf-core/star/align/star-align.diff index ed59490be..765781007 100644 --- a/modules/nf-core/star/align/star-align.diff +++ b/modules/nf-core/star/align/star-align.diff @@ -9,9 +9,9 @@ Changes in 'star/align/main.nf': conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/101ea47973178f85ff66a34de6a7462aaf99d947d3924c27ce8a2d5a63009065/data' : -- 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' }" -+ container 'nf-core/htslib_samtools_star_gawk:311d422a50e6d829' +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/26/268b4c9c6cbf8fa6606c9b7fd4fafce18bf2c931d1a809a0ce51b105ec06c89d/data' : +- 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' }" ++ container 'nf-core/htslib_samtools_star_gawk:ae438e9a604351a4' input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 4402ff963..ac16acfe6 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -3,7 +3,7 @@ process STAR_GENOMEGENERATE { label 'process_high' conda "${moduleDir}/environment.yml" - container 'nf-core/htslib_samtools_star_gawk:311d422a50e6d829' + container 'nf-core/htslib_samtools_star_gawk:ae438e9a604351a4' input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/genomegenerate/star-genomegenerate.diff b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff index 85f11ae52..a479a399d 100644 --- a/modules/nf-core/star/genomegenerate/star-genomegenerate.diff +++ b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff @@ -9,9 +9,9 @@ Changes in 'star/genomegenerate/main.nf': conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/101ea47973178f85ff66a34de6a7462aaf99d947d3924c27ce8a2d5a63009065/data' : -- 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' }" -+ container 'nf-core/htslib_samtools_star_gawk:311d422a50e6d829' +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/26/268b4c9c6cbf8fa6606c9b7fd4fafce18bf2c931d1a809a0ce51b105ec06c89d/data' : +- 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' }" ++ container 'nf-core/htslib_samtools_star_gawk:ae438e9a604351a4' input: tuple val(meta), path(fasta)