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🐛 FIX: remove suffix option (#1188)
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1 changed files with 8 additions and 3 deletions
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@ -12,9 +12,7 @@ process LIMA {
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path primers
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path primers
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output:
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output:
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tuple val(meta), path("*.clips") , emit: clips
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tuple val(meta), path("*.counts") , emit: counts
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tuple val(meta), path("*.counts") , emit: counts
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tuple val(meta), path("*.guess") , emit: guess
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tuple val(meta), path("*.report") , emit: report
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tuple val(meta), path("*.report") , emit: report
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tuple val(meta), path("*.summary"), emit: summary
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tuple val(meta), path("*.summary"), emit: summary
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path "versions.yml" , emit: versions
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path "versions.yml" , emit: versions
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@ -27,10 +25,18 @@ process LIMA {
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tuple val(meta), path("*.fastq.gz") , optional: true, emit: fastqgz
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tuple val(meta), path("*.fastq.gz") , optional: true, emit: fastqgz
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tuple val(meta), path("*.xml") , optional: true, emit: xml
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tuple val(meta), path("*.xml") , optional: true, emit: xml
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tuple val(meta), path("*.json") , optional: true, emit: json
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tuple val(meta), path("*.json") , optional: true, emit: json
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tuple val(meta), path("*.clips") , optional: true, emit: clips
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tuple val(meta), path("*.guess") , optional: true, emit: guess
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script:
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script:
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def args = task.ext.args ?: ''
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def prefix = task.ext.prefix ?: "${meta.id}"
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if( "$ccs" == "${prefix}.bam" ) error "Input and output names are the same, set prefix in module configuration"
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if( "$ccs" == "${prefix}.fasta" ) error "Input and output names are the same, set prefix in module configuration"
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if( "$ccs" == "${prefix}.fasta.gz" ) error "Input and output names are the same, set prefix in module configuration"
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if( "$ccs" == "${prefix}.fastq" ) error "Input and output names are the same, set prefix in module configuration"
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if( "$ccs" == "${prefix}.fastq.gz" ) error "Input and output names are the same, set prefix in module configuration"
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"""
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"""
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OUT_EXT=""
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OUT_EXT=""
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@ -46,7 +52,6 @@ process LIMA {
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OUT_EXT="fastq.gz"
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OUT_EXT="fastq.gz"
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fi
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fi
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echo \$OUT_EXT
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lima \\
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lima \\
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$ccs \\
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$ccs \\
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$primers \\
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$primers \\
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