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Make gff a param and not an optional input

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Anders Goncalves da Silva 2021-02-15 11:50:52 -08:00
parent 4af7414419
commit e8d1171b5d
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1 changed files with 2 additions and 5 deletions
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7
software/ivar/variants/main.nf
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@ -22,7 +22,6 @@ process IVAR_VARIANTS {
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
path fasta path fasta
path gff_file
output: output:
tuple val(meta), path("*.tsv"), emit: variants tuple val(meta), path("*.tsv"), emit: variants
@ -32,10 +31,8 @@ process IVAR_VARIANTS {
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : "" def save_mpileup = params.containsKey('save_mpileup') ? "tee ${prefix}.mpileup |" : ""
// the gff file is optional, so following the pattern suggested here: def gff = params.containsKey('gff') ? "-g ${params.get('gff')}" : ""
//https://github.com/nextflow-io/patterns/blob/master/docs/optional-input.adoc
def gff = gff_file.name != 'NO_FILE' ? "-g $gff_file" : ""
""" """
samtools mpileup \\ samtools mpileup \\
$options.args2 \\ $options.args2 \\