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Merge pull request #1703 from drpatelh/star

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Bump container version for STAR to 2.7.10a
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Harshil Patel 2022-05-27 12:29:59 +01:00 committed by GitHub
commit b86d792055
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3 changed files with 18 additions and 18 deletions
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13
modules/star/align/main.nf
View file

@ -2,16 +2,15 @@ process STAR_ALIGN {
tag "$meta.id" tag "$meta.id"
label 'process_high' label 'process_high'
// Note: 2.7X indices incompatible with AWS iGenomes. conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
conda (params.enable_conda ? 'bioconda::star=2.7.9a' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/star:2.7.9a--h9ee0642_0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' :
'quay.io/biocontainers/star:2.7.9a--h9ee0642_0' }" 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)
path index path index
path gtf path gtf
val star_ignore_sjdbgtf val star_ignore_sjdbgtf
val seq_platform val seq_platform
val seq_center val seq_center
@ -67,6 +66,8 @@ process STAR_ALIGN {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
star: \$(STAR --version | sed -e "s/STAR_//g") star: \$(STAR --version | sed -e "s/STAR_//g")
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS END_VERSIONS
""" """
} }

13
modules/star/genomegenerate/main.nf
View file

@ -2,19 +2,18 @@ process STAR_GENOMEGENERATE {
tag "$fasta" tag "$fasta"
label 'process_high' label 'process_high'
// Note: 2.7X indices incompatible with AWS iGenomes. conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
conda (params.enable_conda ? "bioconda::star=2.7.9a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1c4c32d87798d425c970ececfbadd155e7560277-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' :
'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1c4c32d87798d425c970ececfbadd155e7560277-0' }" 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }"
input: input:
path fasta path fasta
path gtf path gtf
output: output:
path "star" , emit: index path "star" , emit: index
path "versions.yml" , emit: versions path "versions.yml", emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
@ -22,7 +21,7 @@ process STAR_GENOMEGENERATE {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def args_list = args.tokenize() def args_list = args.tokenize()
def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
if (args_list.contains('--genomeSAindexNbases')) { if (args_list.contains('--genomeSAindexNbases')) {
""" """
mkdir star mkdir star

10
tests/modules/star/align/test.yml
View file

@ -36,7 +36,7 @@
- path: output/star/star/transcriptInfo.tab - path: output/star/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36 md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/star/test.Aligned.out.bam - path: output/star/test.Aligned.out.bam
md5sum: b9f5e2f6a624b64c300fe25dc3ac801f md5sum: 63de6af2210e138b49d7b4d570c6e67f
- path: output/star/test.Log.final.out - path: output/star/test.Log.final.out
- path: output/star/test.Log.out - path: output/star/test.Log.out
- path: output/star/test.Log.progress.out - path: output/star/test.Log.progress.out
@ -80,7 +80,7 @@
- path: output/star/star/transcriptInfo.tab - path: output/star/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36 md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/star/test.Aligned.out.bam - path: output/star/test.Aligned.out.bam
md5sum: 38d08f0b944a2a1b981a250d675aa0d9 md5sum: 7cdef439bc8092bfefb4d091bf8ee6ab
- path: output/star/test.Log.final.out - path: output/star/test.Log.final.out
- path: output/star/test.Log.out - path: output/star/test.Log.out
- path: output/star/test.Log.progress.out - path: output/star/test.Log.progress.out
@ -124,7 +124,7 @@
- path: output/star/star/transcriptInfo.tab - path: output/star/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36 md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/star/test.Aligned.out.bam - path: output/star/test.Aligned.out.bam
md5sum: c740d5177067c1fcc48ab7a16cd639d7 md5sum: 5dbc36fce7b72628c809bbc7d3d67973
- path: output/star/test.Log.final.out - path: output/star/test.Log.final.out
- path: output/star/test.Log.out - path: output/star/test.Log.out
- path: output/star/test.Log.progress.out - path: output/star/test.Log.progress.out
@ -168,9 +168,9 @@
- path: output/star/star/transcriptInfo.tab - path: output/star/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36 md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/star/test.Aligned.out.bam - path: output/star/test.Aligned.out.bam
md5sum: a1bd1b40950a58ea2776908076160052 md5sum: d85858bf55a523121dde762046a34c5c
- path: output/star/test.Chimeric.out.junction - path: output/star/test.Chimeric.out.junction
md5sum: 327629eb54032212f29e1c32cbac6975 md5sum: ae87d1a24180f5a35cf6b47fdfdd0539
- path: output/star/test.Log.final.out - path: output/star/test.Log.final.out
- path: output/star/test.Log.out - path: output/star/test.Log.out
- path: output/star/test.Log.progress.out - path: output/star/test.Log.progress.out