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Bug fixes
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parent
a1b705d412
commit
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1 changed files with 6 additions and 5 deletions
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@ -8,10 +8,10 @@ process RSEM_CALCULATEEXPRESSION {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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container "quay.io/biocontainers/rsem:1.3.3--pl526ha52163a_0"
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//container "https://depot.galaxyproject.org/singularity/rsem:1.3.3--pl526ha52163a_0"
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container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
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//container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
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conda (params.conda ? "bioconda::rsem=1.3.3" : null)
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conda (params.conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
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input:
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tuple val(meta), path(reads)
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@ -22,6 +22,7 @@ process RSEM_CALCULATEEXPRESSION {
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tuple val(meta), path("*.genes.results") , emit: counts_gene
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tuple val(meta), path("*.isoforms.results"), emit: counts_transcript
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tuple val(meta), path("*.stat") , emit: stat
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tuple val(meta), path("*.log") , emit: logs
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path "*.version.txt" , emit: version
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tuple val(meta), path("*.STAR.genome.bam") , optional:true, emit: bam_star
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@ -32,7 +33,7 @@ process RSEM_CALCULATEEXPRESSION {
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def strandedness = ''
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if (meta.strandedness == 'forward') {
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strandedness = '--strandedness forward'
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@ -45,8 +46,8 @@ process RSEM_CALCULATEEXPRESSION {
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rsem-calculate-expression \\
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--num-threads $task.cpus \\
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--temporary-folder ./tmp/ \\
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$paired_end \\
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$strandedness \\
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$paired_end \\
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$ioptions.args \\
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$reads \\
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\$INDEX \\
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