From 1d9c4ba6b152fd16f903f924e8b380aed79e165c Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Tue, 31 Jul 2018 16:01:31 +0200
Subject: [PATCH] new pipeline_bowtie2_nosplit bam
---
src/RNAseq_sen1D_bowtie2_nosplit.config | 143 ++++++++++++++++++++++++
1 file changed, 143 insertions(+)
create mode 100644 src/RNAseq_sen1D_bowtie2_nosplit.config
diff --git a/src/RNAseq_sen1D_bowtie2_nosplit.config b/src/RNAseq_sen1D_bowtie2_nosplit.config
new file mode 100644
index 0000000..ce64be9
--- /dev/null
+++ b/src/RNAseq_sen1D_bowtie2_nosplit.config
@@ -0,0 +1,143 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $fastqc_fastq {
+ container = "fastqc:0.11.5"
+ }
+ $fastqc_fastq_cutadapt {
+ container = "fastqc:0.11.5"
+ }
+ $fastqc_fastq_randombp {
+ container = "fastqc:0.11.5"
+ }
+ $fastqc_fastq_urqt {
+ container = "fastqc:0.11.5"
+ }
+ $adaptor_removal {
+ container = "cutadapt:1.14"
+ }
+ $multiqc {
+ container = "multiqc:1.0"
+ }
+ $random_bases_4_trimming {
+ container = "cutadapt:1.14"
+ }
+ $trimming {
+ container = "urqt:d62c1f8"
+ }
+ $index_fasta {
+ container = "bowtie2:2.3.4.1"
+ }
+ $mapping_fastq {
+ container = "bowtie2:2.3.4.1"
+ }
+ $sort_bam {
+ container = "samtools:1.7"
+ }
+ $index_bam {
+ container = "samtools:1.7"
+ }
+ }
+ }
+ sge {
+ process{
+ $fastqc_fastq {
+ beforeScript = "module purge; module load FastQC/0.11.5"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ $fastqc_fastq_cutadapt {
+ beforeScript = "module purge; module load FastQC/0.11.5"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ $fastqc_fastq_randombp {
+ beforeScript = "module purge; module load FastQC/0.11.5"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ $fastqc_fastq_urqt {
+ beforeScript = "module purge; module load FastQC/0.11.5"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ $multiqc {
+ beforeScript = "module purge; module load FastQC/1.0"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ $adaptor_removal {
+ beforeScript = "module purge; module load cutadapt/1.14"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ $random_bases_4_trimming {
+ beforeScript = "module purge; module load cutadapt/1.14"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ $trimming {
+ beforeScript = "module purge; module load UrQt/d62c1f8"
+ executor = "sge"
+ cpus = 4
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ $index_fasta {
+ beforeScript = "module purge; module load Bowtie2/2.3.4.1"
+ }
+ $mapping_fastq {
+ beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
+ }
+ $sort_bam {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ }
+ $index_bam {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ }
+ }
+ }
+}
--
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