From 5f09fa599b47d97eaac84a35257eb32b4650c0f3 Mon Sep 17 00:00:00 2001
From: Claude Jean-Baptiste <jclaud01@pxe.cbp.ens-lyon.fr>
Date: Wed, 20 Jun 2018 19:05:27 +0200
Subject: [PATCH] dd bowtie1
---
src/RNAseq_jbc.config | 7 ++++++-
src/RNAseq_jbc.nf | 12 ++++++------
src/docker_modules/RSEM/1.3.0/Dockerfile | 2 +-
src/docker_modules/file_handle/0.1.1/Dockerfile | 2 +-
4 files changed, 14 insertions(+), 9 deletions(-)
diff --git a/src/RNAseq_jbc.config b/src/RNAseq_jbc.config
index 5b9628c..a703fe3 100644
--- a/src/RNAseq_jbc.config
+++ b/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"
+ }
+ $trimming2 {
container = "urqt:d62c1f8"
}
- }
+ }
}
sge {
process{
diff --git a/src/RNAseq_jbc.nf b/src/RNAseq_jbc.nf
index c11ebce..33ff986 100644
--- a/src/RNAseq_jbc.nf
+++ b/src/RNAseq_jbc.nf
@@ -11,7 +11,7 @@
* for paired-end data
*/
-params.fastq = "$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
diff --git a/src/docker_modules/RSEM/1.3.0/Dockerfile b/src/docker_modules/RSEM/1.3.0/Dockerfile
index 1ccdaa7..3efcb08 100644
--- a/src/docker_modules/RSEM/1.3.0/Dockerfile
+++ b/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* \
diff --git a/src/docker_modules/file_handle/0.1.1/Dockerfile b/src/docker_modules/file_handle/0.1.1/Dockerfile
index 0557983..fcec296 100644
--- a/src/docker_modules/file_handle/0.1.1/Dockerfile
+++ b/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
--
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