fix beug for psmn

src/RNAseq.config

@@ -27,6 +27,7 @@ profiles {
         clusterOptions = "-cwd -V"
         memory = "20GB"
         cpus = 16
+	penv = 'openmp16'
         time = "12h"
         queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
         penv = 'openmp16'
@@ -42,8 +43,7 @@ profiles {
         queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
       withName: counting {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "htseq/0.11.2"
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules; module purge; module load htseq/0.11.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1
@@ -51,6 +51,17 @@ profiles {
         time = "12h"
         queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
       }
+      withName: coverage{
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "deeptools/3.0.2"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+	penv = 'openmp16'
+        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+     }
     }
   }
   docker {

src/RNAseq.nf

@@ -4,6 +4,10 @@
 
 params.fastq_raw = "data/demultiplexed/*{_R1,_R2}.fastq.gz"
 params.output = "results"
+params.script_cov = "src/norm_coverage.sh"
+
+log.info "script for coverage : ${script_cov}"
+
 
 Channel
    .fromFilePairs(params.fastq_raw)
@@ -27,8 +31,7 @@ process trimming {
 
   script:
   """
-  cutadapt -a AGATCGGAAGAGC -A AGATCGGAAGAGC \
-  --minimum-length 50 \
+  cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
   -o ${file_id}_cut_R1.fastq.gz -p ${file_id}_tmp_R2.fastq.gz \
   ${reads[0]} ${reads[1]} > ${file_id}_report.txt
 
@@ -129,7 +132,7 @@ samtools index ${file_id}_sorted.bam
 """
 }
 
-sorted_bam_files.into{sorted_bam_htseq, sorted_bam_coverage}
+sorted_bam_files.into{sorted_bam_htseq; sorted_bam_coverage}
 
 /*                   HTseq                            */
 
@@ -190,19 +193,25 @@ htseq-count ${bam[0]} ${gtf} \
 """
 }
 
+Channel
+   .fromFilePairs(params.script_cov)
+   .ifEmpty { error "Cannot find any file matching: ${params.script_cov}" }
+   .set {script_channel}
+
 process coverage {
   tag "$file_id"
   publishDir "${params.output}/05_coverage/", mode: 'copy'
 
   input:
   set file_id, file(bam) from sorted_bam_coverage
+  set script from script_channel.collect()
 
   output:
   file "*.bw" into coverage_files
 
   script:
 """
-bash src/norm_coverage.sh -b ${bam} \
+bash ${script} -b ${bam} \
                           -o {file_id}.bw \
                           --binSize 1 \
                           -p ${cpus} 8

src/RNAseq_illumina.nf

@@ -4,6 +4,10 @@
 
 params.fastq_raw = "data/demultiplexed/*{_R1,_R2}.fastq.gz"
 params.output = "results"
+params.script_cov = "src/norm_coverage.sh"
+
+log.info "script for coverage : ${params.script_cov}"
+
 
 Channel
    .fromFilePairs(params.fastq_raw)
@@ -127,6 +131,7 @@ samtools index ${file_id}_sorted.bam
 """
 }
 
+sorted_bam_files.into{sorted_bam_htseq; sorted_bam_coverage}
 
 /*                   HTseq                            */
 
@@ -134,7 +139,7 @@ process sort_bam {
   tag "$file_id"
 
   input:
-    set file_id, file(bam) from sorted_bam_files
+    set file_id, file(bam) from sorted_bam_htseq
 
   output:
     set file_id, "*_htseq.bam" into sorted_bam_files_2
@@ -186,3 +191,28 @@ htseq-count ${bam[0]} ${gtf} \
 
 """
 }
+
+Channel
+   .fromPath(params.script_cov)
+   .ifEmpty { error "Cannot find any file matching: ${params.script_cov}" }
+   .set {script_channel}
+
+process coverage {
+  tag "$file_id"
+  publishDir "${params.output}/05_coverage/", mode: 'copy'
+
+  input:
+  set file_id, file(bam) from sorted_bam_coverage
+  set script from script_channel.collect()
+
+  output:
+  file "*.bw" into coverage_files
+
+  script:
+"""
+bash ${script} -b ${bam[0]} \
+                          -o ${file_id}.bw \
+                          --binSize 1 \
+                          -p ${task.cpus}
+"""
+}

src/norm_coverage.sh

@@ -2,33 +2,42 @@
 
 set -e
 
-usage() { echo "Usage: $0 -b <bamfile.bam> -o <outputName> --binSize <int> -p <CPUs>" 1>&2; exit 1; }
+usage() { echo "Usage: $0 -b <bamfile.bam> -o <outputName> -s <binSize> -p <CPUs>" 1>&2; exit 1; }
 
 cpus=4
 binSize=1
 
-while getopts "b:o:binSize:p:" arg; do
+while getopts "hb:o:s:p:" arg; do
   case $arg in
-    -h)
-      echo "usage"
+    h)
+      usage
       ;;
-    -b)
+    b)
       bam=$OPTARG
       ;;
-    -o)
+    o)
       output=$OPTARG
       ;;
-    --binSize)
+    s)
       binSize=$OPTARG
       ;;
-    -p)
+    p)
       cpus=$OPTARG
       ;;
+    \?)
+      echo "$OPTARG : invalid option"
+      usage
+      ;;
+     :)
+      echo "$OPTARG requiert an argument"
+      usage
+      ;;
+
   esac
 done
 
 hg38=$(samtools view ${bam} | awk '{print $1}' | sort | uniq | wc -l)
 factor=$(echo "1000000/($hg38)" | bc -l)
 echo "hg38 counts : $hg38"
-echo "scaling factor : $factor\n"
-bamCoverage -p ${cpus} --scaleFactor ${factor} --binSize ${binSize} -b ${bam} -o ${output}
+echo "scaling factor : $factor"
+echo "bamCoverage -p ${cpus} --scaleFactor ${factor} --binSize ${binSize} -b ${bam} -o ${output}"