05operateurs

Nextflow/05operateurs/operateur.collect.nf

@@ -3,17 +3,17 @@ nextflow.enable.dsl=2
 chanFastq = Channel.fromPath( './rawdata/dev/control/SRR*_{1,2}.fastq.gz', checkIfExists: true)
 
 process collectme {
-	publishDir('result')
+	publishDir('result/05operateurs')
 
 	input:
 	path(reads)
 
 	output:
-	path('*.fastq', emit: outfile)
+	path('collect.log', emit: outfile)
 
 	script:
 	"""
-ls -l *.gz > list.fastq
+ls -l *.gz > collect.log
 	"""
 }
 

Nextflow/05operateurs/operateur.collect2.nf

@@ -4,18 +4,18 @@ test = Channel.fromPath('./rawdata/dev/control/*.fastq.gz')
 
 
 process gunzip {
-	publishDir('result')
+	publishDir('result/05operateurs/')
 
 	input:
 	val(par)
 
 	output:
-	path('log')
+	path('collect2.log')
 
 	script:
 	println(par.join(' '))
 	"""
-echo $par > log
+echo $par > collect2.log
 	"""
 }
 

Nextflow/05operateurs/operateur.grouptuple.nf

@@ -2,8 +2,7 @@ nextflow.enable.dsl=2
 
 chanFastq = Channel.fromPath( './dataset.csv' ).splitCsv(header: ['sample', 'fileR1', 'fileR2'])
 
-//chanFastq.view()
-
+//chanFastq.view { "[channel] csv:$it" }
 //chanFastq.map {[it.sample,[it.fileR1, it.fileR2]]}.groupTuple().view()
 
 
@@ -15,11 +14,11 @@ process mock1 {
 
 	output:
 	tuple val(sample), path('*.sam'), emit: outfile
-	path('*.sh'), emit: debug
+	tuple val(sample), path('mock.sh'), emit: debug
 
 	script:
 	"""
-echo "bwa genome ${read1} ${read2} > ${sample}.sam" > mock.sh
+echo "bwa genome ${read1} ${read2} > ${read1}.sam" > mock.sh
 touch ${read1}.sam
 	"""
 }
@@ -31,8 +30,7 @@ process mock2 {
 	tuple val(sample), path(sam)
 
 	output:
-	tuple val(sample), path('*merged.sam'), emit: outfile
-	path('*.sh'), emit: debug optional true
+	tuple val(sample), path('*merged.sam'), path('mock.sh'), emit: outfile
 
 	script:
 	if(sam.collect().size > 1) {
@@ -43,6 +41,7 @@ touch ${sample}.merged.sam
 	}
 	else {
 	"""
+echo "cp ${sam} ${sample}.merged.sam" > mock.sh
 touch ${sample}.merged.sam
     """
 	}
@@ -51,9 +50,8 @@ touch ${sample}.merged.sam
 
 workflow {
 	mock1(chanFastq)
-	//mock1.out.debug.view()
-	//mock1.out.outfile.view()
+	mock1.out.debug.view { sample, script -> "[mock1] sample: ${sample} \t script: $script" }
+	mock1.out.outfile.view { sample, file -> "[mock1] sample: ${sample} \t file:${file}" }
 	mock2(mock1.out.outfile.groupTuple())
-	//mock2.out.debug.view()
-	mock2.out.outfile.view()
+    mock2.out.outfile.view { sample, file, script -> "[mock2] sample: ${sample} \t file:${file} \t script: ${script}" }
 }