From fb6c7bca3d55c19a793372513395e3a567bdd7ba Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 27 May 2022 11:35:04 +0100 Subject: [PATCH] Bump container version for STAR to 2.7.10a --- modules/star/align/main.nf | 13 +++++++------ modules/star/genomegenerate/main.nf | 13 ++++++------- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/modules/star/align/main.nf b/modules/star/align/main.nf index 762b84f6..e5aa36f5 100644 --- a/modules/star/align/main.nf +++ b/modules/star/align/main.nf @@ -2,16 +2,15 @@ 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) - path index - path gtf + path index + path gtf val star_ignore_sjdbgtf val seq_platform val seq_center @@ -67,6 +66,8 @@ process STAR_ALIGN { cat <<-END_VERSIONS > versions.yml "${task.process}": star: \$(STAR --version | sed -e "s/STAR_//g") + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') END_VERSIONS """ } diff --git a/modules/star/genomegenerate/main.nf b/modules/star/genomegenerate/main.nf index e5568f1d..3c298016 100644 --- a/modules/star/genomegenerate/main.nf +++ b/modules/star/genomegenerate/main.nf @@ -2,19 +2,18 @@ process STAR_GENOMEGENERATE { tag "$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 path gtf output: - path "star" , emit: index - path "versions.yml" , emit: versions + path "star" , emit: index + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -22,7 +21,7 @@ process STAR_GENOMEGENERATE { script: def args = task.ext.args ?: '' 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')) { """ mkdir star