Commit b9cd2942 authored by Ludovic Legrand's avatar Ludovic Legrand
Browse files

uniformisation des publishdir

parent 913417c0
...@@ -22,7 +22,7 @@ bwa index $genome ...@@ -22,7 +22,7 @@ bwa index $genome
process mapping { process mapping {
publishDir("${params.outdir}/01.mapping") publishDir("${params.outdir}/conf.conda1/01.mapping")
tag("${id}") tag("${id}")
label "multithread" label "multithread"
......
...@@ -20,7 +20,7 @@ bwa index $genome ...@@ -20,7 +20,7 @@ bwa index $genome
process mapping { process mapping {
publishDir("${params.outdir}/01.mapping") publishDir("${params.outdir}/conf.conda2/01.mapping")
tag("${id}") tag("${id}")
label "multithread" label "multithread"
......
...@@ -4,7 +4,7 @@ version = ['1.9','1.1'] ...@@ -4,7 +4,7 @@ version = ['1.9','1.1']
process softwareVersions { process softwareVersions {
label "local" label "local"
publishDir "${params.outdir}/", mode: 'copy' publishDir "${params.outdir}/conf.env/", mode: 'copy'
conda "bwa samtools=${samtoolsVersion}" conda "bwa samtools=${samtoolsVersion}"
......
...@@ -3,7 +3,7 @@ nextflow.enable.dsl=2 ...@@ -3,7 +3,7 @@ nextflow.enable.dsl=2
chanFastq = Channel.fromFilePairs( params.reads, size: 2, checkIfExists: true) //change chanFastq = Channel.fromFilePairs( params.reads, size: 2, checkIfExists: true) //change
process gunzip { process gunzip {
publishDir(params.outdir) //change publishDir("${params.outdir}/conf.simple/)
tag("${id}") // id correspond a la variable dans input tag("${id}") // id correspond a la variable dans input
label 'multithread' label 'multithread'
...@@ -24,7 +24,7 @@ touch myfile ...@@ -24,7 +24,7 @@ touch myfile
} }
process gzip { process gzip {
publishDir("$params.outdir") // change publishDir("${params.outdir}/conf.simple/") // change
tag("${reads}") tag("${reads}")
input: input:
......
params { params {
reads = './rawdata/dev/control/SRR*_{1,2}.fastq.gz' reads = './rawdata/dev/control/SRR*_{1,2}.fastq.gz'
outdir = 'result/conf_env' outdir = 'result/'
} }
timeline { timeline {
enabled = true enabled = true
......
...@@ -3,7 +3,7 @@ nextflow.enable.dsl=2 ...@@ -3,7 +3,7 @@ nextflow.enable.dsl=2
chanFastq = Channel.fromPath( './rawdata/dev/control/SRR*_{1,2}.fastq.gz', checkIfExists: true) chanFastq = Channel.fromPath( './rawdata/dev/control/SRR*_{1,2}.fastq.gz', checkIfExists: true)
process collectme { process collectme {
publishDir('result/05operateurs') publishDir('result/operateur.collect/')
input: input:
path(reads) path(reads)
......
...@@ -4,7 +4,7 @@ test = Channel.fromPath('./rawdata/dev/control/*.fastq.gz') ...@@ -4,7 +4,7 @@ test = Channel.fromPath('./rawdata/dev/control/*.fastq.gz')
process gunzip { process gunzip {
publishDir('result/05operateurs/') publishDir('result/operateur.collect2/')
input: input:
val(par) val(par)
......
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