amelioration de 04config

Nextflow/04configuration_environnement/conf.executor.nf → Nextflow/04configuration_environnement/conf.conda1.nf

 nextflow.enable.dsl=2
 
 chanFastq = Channel.fromFilePairs( params.reads, size: 2, checkIfExists: true)
-modeList = ['multithread', 'local']
 
 process index {
 	storeDir 'indices/bwa'
@@ -15,6 +14,7 @@ process index {
 	path("$genome*", emit: indices)
 	
 	script:
+	println("[default] cpus: ${task.cpus}  ;  ${task.memory}")
 	"""
 bwa index $genome
 	"""
@@ -37,6 +37,7 @@ process mapping {
 	path('*.sam')
 
 	script:
+	println("[mutlithread] mapping: ${task.cpus}  ;  ${task.memory}")
 	"""
 bwa mem -t ${task.cpus} ${genome} $reads > ${id}.mapping.sam
 	"""

Nextflow/04configuration_environnement/conf.conda2.nf

+nextflow.enable.dsl=2
+
+chanFastq = Channel.fromFilePairs( params.reads, size: 2, checkIfExists: true)
+
+process index {
+	storeDir 'indices/bwa'
+	
+	input:
+	path(genome)
+	
+	output:
+	path("$genome*", emit: indices)
+	
+	script:
+	println("[default] cpus: ${task.cpus}  ;  ${task.memory}")
+	"""
+bwa index $genome
+	"""
+}
+
+process mapping {
+
+	publishDir("${params.outdir}/01.mapping")
+	tag("${id}")
+	label "multithread"
+		
+	input:
+	tuple val(id), path(reads)
+	path(index)
+	path(genome)
+
+	output:
+	path('*.sam')
+	path('mapping.version')
+
+	script:
+	println("[mutlithread] mapping: ${task.cpus}  ;  ${task.memory}")
+	"""
+bwa 2>&1 | grep -i version > mapping.version
+bwa mem -t ${task.cpus} ${genome} $reads > ${id}.mapping.sam
+	"""
+}
+
+workflow {
+	index(params.genome)
+	mapping(chanFastq, index.out.indices, params.genome)
+}

Nextflow/04configuration_environnement/conf.simple.nf

@@ -5,6 +5,7 @@ chanFastq = Channel.fromFilePairs( params.reads, size: 2, checkIfExists: true) /
 process gunzip {
 	publishDir(params.outdir) //change
 	tag("${id}") // id correspond a la variable dans input
+	label 'multithread'
 
 	input:
 	tuple val(id), path(reads)
@@ -13,8 +14,7 @@ process gunzip {
 	path('*.fastq')
 
 	script:
-// ici du groovy
-    println("groovy: " + id)
+    println("[multithread] fastqID: ${id}  ;  cpus: ${task.cpus}  ;  executor: $task.executor")
 	"""
 # ici ce qui me plait, par défaut du bash
 #!/usr/bin/env bash
@@ -34,6 +34,7 @@ process gzip {
     path('*.fastq.gz')
 
     script:
+    println("[default] fastq: ${reads}  ;  cpus: ${task.cpus}  ;  executor: $task.executor")
     """
 #!/usr/bin/env bash
 gzip -kc ${reads} > ${reads}.gz

Nextflow/04configuration_environnement/nextflow.config

 params {
 	reads  = './rawdata/dev/control/SRR*_{1,2}.fastq.gz'
-	genome = 'genome.fasta'
-	outdir = 'result' 
+	outdir = 'result/conf_env' 
 }
 timeline {
   enabled = true
@@ -28,7 +27,6 @@ conda {
 
 
 // profiles
-
 profiles {
     standard {
         includeConfig 'conf/lipm-smp.config'
@@ -45,4 +43,26 @@ profiles {
     genologin {
         includeConfig 'conf/genotoul-slurm.config'
     }
+    
+    conda {
+		process {
+			withName: 'index|mapping' {
+				conda = 'bwa'
+			}
+		}
+    }
+    
+    singularity {
+    	process {
+			withName: 'index|mapping' {
+				//container = 'docker://quay.io/biocontainers/bwa:0.7.17--h5bf99c6_8'
+				container = 'img/bwa:0.7.17--h5bf99c6_8'
+			}
+		}
+		singularity {
+			enabled = true
+		}
+
+    }
+
 }