chore: Replace results dir with parameterized outdir
This commit is contained in:
parent
b415c29ec0
commit
93bd5cedec
10 changed files with 10 additions and 10 deletions
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@ -13,7 +13,7 @@ process CLIQUESNV {
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tuple val(prefix), path("*.json")
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tuple val(prefix), path("*.json")
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tuple val(prefix), path("*.fasta")
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tuple val(prefix), path("*.fasta")
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publishDir "results/${task.process}", mode: 'copy'
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publishDir "${params.outdir}/${task.process}", mode: 'copy'
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when:
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when:
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task.ext.when == null || task.ext.when
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task.ext.when == null || task.ext.when
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@ -7,7 +7,7 @@ process EFETCH {
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input:
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input:
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val(genome)
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val(genome)
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publishDir "results", mode: 'copy'
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publishDir "${params.outdir}", mode: 'copy'
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output:
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output:
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path 'reference.fasta'
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path 'reference.fasta'
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@ -12,7 +12,7 @@ process HAPLINK_HAPLOTYPES {
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output:
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output:
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tuple val(prefix), path("*.yaml")
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tuple val(prefix), path("*.yaml")
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publishDir "results/${task.process}", mode: 'copy'
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publishDir "${params.outdir}/${task.process}", mode: 'copy'
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when:
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when:
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task.ext.when == null || task.ext.when
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task.ext.when == null || task.ext.when
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@ -12,7 +12,7 @@ process HAPLINK_SEQUENCES {
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output:
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output:
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tuple val(prefix), val(method), path("*.fasta")
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tuple val(prefix), val(method), path("*.fasta")
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publishDir "results/${method}", mode: 'copy'
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publishDir "${params.outdir}/${method}", mode: 'copy'
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when:
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when:
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task.ext.when == null || task.ext.when
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task.ext.when == null || task.ext.when
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@ -12,7 +12,7 @@ process HAPLINK_VARIANTS {
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output:
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output:
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tuple val(prefix), path("*.vcf")
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tuple val(prefix), path("*.vcf")
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publishDir "results/${task.process}", mode: 'copy'
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publishDir "${params.outdir}/${task.process}", mode: 'copy'
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when:
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when:
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task.ext.when == null || task.ext.when
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task.ext.when == null || task.ext.when
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@ -8,7 +8,7 @@ process MINIMAP2 {
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tuple val(prefix), path(reads)
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tuple val(prefix), path(reads)
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path reference
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path reference
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publishDir "results", mode: 'copy'
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publishDir "${params.outdir}", mode: 'copy'
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output:
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output:
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tuple val(prefix), path("*.bam"), path("*.bam.bai")
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tuple val(prefix), path("*.bam"), path("*.bam.bai")
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@ -11,7 +11,7 @@ process QUASIRECOMB {
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output:
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output:
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tuple val(prefix), path("*.fasta")
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tuple val(prefix), path("*.fasta")
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publishDir "results/${task.process}", mode: 'copy'
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publishDir "${params.outdir}/${task.process}", mode: 'copy'
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when:
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when:
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task.ext.when == null || task.ext.when
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task.ext.when == null || task.ext.when
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@ -13,7 +13,7 @@ process SHORAH_AMPLICON {
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tuple val(prefix), path("*.vcf")
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tuple val(prefix), path("*.vcf")
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tuple val(prefix), path("*support.fas")
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tuple val(prefix), path("*support.fas")
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publishDir "results/${task.process}", mode: 'copy'
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publishDir "${params.outdir}/${task.process}", mode: 'copy'
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when:
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when:
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task.ext.when == null || task.ext.when
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task.ext.when == null || task.ext.when
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@ -13,7 +13,7 @@ process SHORAH_SHOTGUN {
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tuple val(prefix), path("*.vcf")
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tuple val(prefix), path("*.vcf")
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tuple val(prefix), path("*support.fas")
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tuple val(prefix), path("*support.fas")
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publishDir "results/${task.process}", mode: 'copy'
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publishDir "${params.outdir}/${task.process}", mode: 'copy'
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when:
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when:
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task.ext.when == null || task.ext.when
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task.ext.when == null || task.ext.when
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@ -12,7 +12,7 @@ process VIQUAS {
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output:
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output:
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tuple val(prefix), path("*.fa")
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tuple val(prefix), path("*.fa")
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publishDir "results/${task.process}", mode: 'copy'
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publishDir "${params.outdir}/${task.process}", mode: 'copy'
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when:
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when:
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task.ext.when == null || task.ext.when
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task.ext.when == null || task.ext.when
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