mapping.nf: fix cpus number

src/mapping.config

@@ -3,7 +3,7 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: mapping_fastq {
+      withname: index_fasta {
         container = "bowtie2:2.3.4.1"
       }
       withname: mapping_fastq {
@@ -19,23 +19,19 @@ profiles {
   }
   psmn {
     process{
-      withname: mapping_fastq {
+      withname: index_fasta {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie2/2.3.4.1"
-        executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
-        memory = "30GB"
-        time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
       withname: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie2/2.3.4.1:SAMtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
         memory = "30GB"
         time = "24h"
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
@@ -46,7 +42,6 @@ profiles {
         module = "sambamba/0.6.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
         memory = "30GB"
         time = "24h"
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
@@ -57,7 +52,6 @@ profiles {
         module = "sambamba/0.6.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
         memory = "30GB"
         time = "24h"
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'

src/mapping.nf

 params.fasta = "$baseDir/data/bam/*.fasta"
 params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
 params.contig = ""
+params.cpus = 10
 
 log.info "fasta files : ${params.fasta}"
 log.info "fastq files : ${params.fastq}"
@@ -37,7 +38,6 @@ cp ${fasta} contigs.fasta
 
 process index_fasta {
   tag "$fasta.baseName"
-  cpus 4
   publishDir "results/mapping/index/", mode: 'copy'
 
   input:
@@ -59,7 +59,7 @@ fi
 
 process mapping_fastq {
   tag "$pair_id"
-  cpus 4
+  cpus params.cpus
 
   input:
   set pair_id, file(reads) from fastq_files
@@ -90,7 +90,8 @@ fi
 
 process sort_bam {
   tag "$file_id"
-  cpus 4
+  cpus params.cpus
+
   publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
@@ -107,7 +108,7 @@ sambamba sort -t ${task.cpus} -o ${file_id}_sorted.bam ${bam}
 
 process index_bam {
   tag "$file_id"
-  cpus 4
+  cpus params.cpus
   publishDir "results/mapping/bams/", mode: 'copy'
 
   input:

src/nf_modules/Bowtie2/indexing.config

@@ -3,7 +3,7 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: mapping_fastq {
+      withname: index_fasta {
         container = "bowtie2:2.3.4.1"
       }
     }
@@ -13,13 +13,11 @@ profiles {
       withname: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie2/2.3.4.1"
-        executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        cpus = 16
-        memory = "30GB"
-        time = "24h"
-        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
-        penv = 'openmp16'
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
       }
     }
   }