millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2025-01-18 02:46:13 -05:00
Code Issues Releases Packages Activity

Bump container version for STAR to 2.7.10a

Browse source
This commit is contained in:
Harshil Patel 2022-05-27 11:35:04 +01:00
parent f89b76afa4
commit fb6c7bca3d
2 changed files with 13 additions and 13 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 "$meta.id" tag "$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
""" """
} }

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

@ -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