millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 11:08:17 +00:00
Code Issues Releases Packages Activity

Merge pull request #1703 from drpatelh/star

Browse source 
Bump container version for STAR to 2.7.10a
This commit is contained in:
Harshil Patel 2022-05-27 12:29:59 +01:00 committed by GitHub
commit b86d792055
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
3 changed files with 18 additions and 18 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

9
modules/star/align/main.nf
View file

@ -2,11 +2,10 @@ process STAR_ALIGN {
tag "$meta.id"
label 'process_high'
// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? 'bioconda::star=2.7.9a' : null)
conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/star:2.7.9a--h9ee0642_0' :
'quay.io/biocontainers/star:2.7.9a--h9ee0642_0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' :
'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }"
input:
tuple val(meta), path(reads)
@ -67,6 +66,8 @@ process STAR_ALIGN {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
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
"""
}

7
modules/star/genomegenerate/main.nf
View file

@ -2,11 +2,10 @@ process STAR_GENOMEGENERATE {
tag "$fasta"
label 'process_high'
// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? "bioconda::star=2.7.9a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1c4c32d87798d425c970ececfbadd155e7560277-0' :
'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1c4c32d87798d425c970ececfbadd155e7560277-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' :
'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }"
input:
path fasta

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

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