dd bowtie1

src/RNAseq_jbc.config

@@ -3,11 +3,16 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
+      $adaptor_removal {
+        container = "cutadapt:1.14"
+      }
       $trimming {
         container = "cutadapt:1.14"
+      }
+      $trimming2 {
         container = "urqt:d62c1f8"
       }
-    }
+     }
   }
   sge {
     process{

src/RNAseq_jbc.nf

@@ -11,7 +11,7 @@
 * for paired-end data
 */
 
-params.fastq = "$baseDir/data/fastq/*_R{1,2}.fastq"
+params.fastq = "/home/jclaud01/Nextflow/nextflow/data/fastq/*_R{1,2}.fastq"
 
 log.info "fastq files : ${params.fastq}"
 
@@ -43,11 +43,11 @@ process adaptor_removal {
 /* for paired-end data */
 
 process trimming {
-  tag "$pair_id"
+  tag "$pair_id2"
   publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
-  set pair_id, file(reads) from fastq_files_cut
+  set pair_id2, file(reads) from fastq_files_cut
 
   output:
   file "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
@@ -65,13 +65,13 @@ process trimming {
 /* for paired-end data */
 
 
-process trimming {
-  tag "${reads}"
+process trimming2 {
+  tag "${pair_id3}"
   cpus 4
   publishDir "results/fastq/trimming2/", mode: 'copy'
 
   input:
-  set pair_id, file(reads) from fastq_files_trim
+  set pair_id3, file(reads) from fastq_files_trim
 
   output:
   file "*_trim2_R{1,2}.fastq.gz" into fastq_files_trim2

src/docker_modules/RSEM/1.3.0/Dockerfile

@@ -4,7 +4,7 @@ MAINTAINER Laurent Modolo
 ENV RSEM_VERSION=1.3.0
 ENV BOWTIE2_VERSION=2.3.4.1
 ENV SAMTOOLS_VERSION=1.7
-ENV PACKAGES git=1:2.17.0* \
+ENV PACKAGES git=1:2.17.1* \
    build-essential=12.4* \
    ca-certificates=20180409 \
    zlib1g-dev=1:1.2.11* \

src/docker_modules/file_handle/0.1.1/Dockerfile

@@ -2,7 +2,7 @@ FROM ubuntu:18.04
 MAINTAINER Laurent Modolo
 
 ENV FILE_HANDLE_VERSION 0.1.1
-ENV PACKAGES git=1:2.17.0* \
+ENV PACKAGES git=1:2.17.1* \
     ca-certificates=20180409