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Update SortMeRNA to 4.3.4 (#790)

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Harshil Patel 2021-10-05 10:36:14 +01:00 committed by GitHub
parent 515793c73e
commit a38508fcbb
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1 changed files with 8 additions and 8 deletions
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16
modules/sortmerna/main.nf
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@ -11,11 +11,11 @@ process SORTMERNA {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::sortmerna=4.2.0" : null)
conda (params.enable_conda ? "bioconda::sortmerna=4.3.4" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--0"
container "https://depot.galaxyproject.org/singularity/sortmerna:4.3.4--h9ee0642_0"
} else {
container "quay.io/biocontainers/sortmerna:4.2.0--0"
container "quay.io/biocontainers/sortmerna:sortmerna:4.3.4--h9ee0642_0"
}
input:
@ -40,12 +40,12 @@ process SORTMERNA {
--other non_rRNA_reads \\
$options.args
gzip -f < non_rRNA_reads.fq > ${prefix}.fastq.gz
mv non_rRNA_reads.fq.gz ${prefix}.fastq.gz
mv rRNA_reads.log ${prefix}.sortmerna.log
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(sortmerna --version 2>&1 | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
END_VERSIONS
"""
} else {
@ -62,13 +62,13 @@ process SORTMERNA {
--out2 \\
$options.args
gzip -f < non_rRNA_reads_fwd.fq > ${prefix}_1.fastq.gz
gzip -f < non_rRNA_reads_rev.fq > ${prefix}_2.fastq.gz
mv non_rRNA_reads_fwd.fq.gz ${prefix}_1.fastq.gz
mv non_rRNA_reads_rev.fq.gz ${prefix}_2.fastq.gz
mv rRNA_reads.log ${prefix}.sortmerna.log
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(sortmerna --version 2>&1 | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
${getSoftwareName(task.process)}: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
END_VERSIONS
"""
}