uniformisation des publishdir

Nextflow/04configuration_environnement/conf.conda1.nf

@@ -22,7 +22,7 @@ bwa index $genome
 
 process mapping {
 
-	publishDir("${params.outdir}/01.mapping")
+	publishDir("${params.outdir}/conf.conda1/01.mapping")
 	tag("${id}")
 	label "multithread"
 	

Nextflow/04configuration_environnement/conf.conda2.nf

@@ -20,7 +20,7 @@ bwa index $genome
 
 process mapping {
 
-	publishDir("${params.outdir}/01.mapping")
+	publishDir("${params.outdir}/conf.conda2/01.mapping")
 	tag("${id}")
 	label "multithread"
 		

Nextflow/04configuration_environnement/conf.env.nf

@@ -4,7 +4,7 @@ version = ['1.9','1.1']
 
 process softwareVersions {
 	label "local"
-	publishDir "${params.outdir}/", mode: 'copy'
+	publishDir "${params.outdir}/conf.env/", mode: 'copy'
 	
 	conda "bwa samtools=${samtoolsVersion}"
 

Nextflow/04configuration_environnement/conf.simple.nf

@@ -3,7 +3,7 @@ nextflow.enable.dsl=2
 chanFastq = Channel.fromFilePairs( params.reads, size: 2, checkIfExists: true) //change
 
 process gunzip {
-	publishDir(params.outdir) //change
+	publishDir("${params.outdir}/conf.simple/)
 	tag("${id}") // id correspond a la variable dans input
 	label 'multithread'
 
@@ -24,7 +24,7 @@ touch myfile
 }
 
 process gzip {
-    publishDir("$params.outdir") // change
+    publishDir("${params.outdir}/conf.simple/") // change
     tag("${reads}")
 
     input:

Nextflow/04configuration_environnement/nextflow.config

 params {
 	reads  = './rawdata/dev/control/SRR*_{1,2}.fastq.gz'
-	outdir = 'result/conf_env' 
+	outdir = 'result/' 
 }
 timeline {
   enabled = true

Nextflow/05operateurs/operateur.collect.nf

@@ -3,7 +3,7 @@ nextflow.enable.dsl=2
 chanFastq = Channel.fromPath( './rawdata/dev/control/SRR*_{1,2}.fastq.gz', checkIfExists: true)
 
 process collectme {
-	publishDir('result/05operateurs')
+	publishDir('result/operateur.collect/')
 
 	input:
 	path(reads)

Nextflow/05operateurs/operateur.collect2.nf

@@ -4,7 +4,7 @@ test = Channel.fromPath('./rawdata/dev/control/*.fastq.gz')
 
 
 process gunzip {
-	publishDir('result/05operateurs/')
+	publishDir('result/operateur.collect2/')
 
 	input:
 	val(par)