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🐛 FIX: remove suffix option (#1188)

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Sébastien Guizard 2021-12-24 11:32:30 +00:00 committed by GitHub
parent cde237e7ce
commit c0e1489133
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1 changed files with 8 additions and 3 deletions
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11
modules/lima/main.nf
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@ -12,9 +12,7 @@ process LIMA {
path primers
output:
tuple val(meta), path("*.clips") , emit: clips
tuple val(meta), path("*.counts") , emit: counts
tuple val(meta), path("*.guess") , emit: guess
tuple val(meta), path("*.report") , emit: report
tuple val(meta), path("*.summary"), emit: summary
path "versions.yml" , emit: versions
@ -27,10 +25,18 @@ process LIMA {
tuple val(meta), path("*.fastq.gz") , optional: true, emit: fastqgz
tuple val(meta), path("*.xml") , optional: true, emit: xml
tuple val(meta), path("*.json") , optional: true, emit: json
tuple val(meta), path("*.clips") , optional: true, emit: clips
tuple val(meta), path("*.guess") , optional: true, emit: guess
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if( "$ccs" == "${prefix}.bam" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fasta" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fasta.gz" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fastq" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fastq.gz" ) error "Input and output names are the same, set prefix in module configuration"
"""
OUT_EXT=""
@ -46,7 +52,6 @@ process LIMA {
OUT_EXT="fastq.gz"
fi
echo \$OUT_EXT
lima \\
$ccs \\
$primers \\