mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
Merge pull request #1703 from drpatelh/star
Bump container version for STAR to 2.7.10a
This commit is contained in:
commit
b86d792055
3 changed files with 18 additions and 18 deletions
|
@ -2,11 +2,10 @@ 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)
|
||||||
|
@ -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
|
||||||
"""
|
"""
|
||||||
}
|
}
|
||||||
|
|
|
@ -2,11 +2,10 @@ 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
|
||||||
|
@ -14,7 +13,7 @@ process STAR_GENOMEGENERATE {
|
||||||
|
|
||||||
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
|
||||||
|
|
|
@ -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
|
||||||
|
|
Loading…
Reference in a new issue