From 09c25a561a3aed25a27320869bb3c37ef75550b9 Mon Sep 17 00:00:00 2001
From: Houry Rana <rhoury@pxe.cbp.ens-lyon.fr>
Date: Fri, 15 Feb 2019 16:31:08 +0100
Subject: [PATCH] :mapping
---
src/RNASeq.config | 27 +++++++++++++++++++++++++++
src/RNASeq.nf | 42 ++++++++++++++++++++++++++++++++++++++++++
2 files changed, 69 insertions(+)
diff --git a/src/RNASeq.config b/src/RNASeq.config
index 0e9552e..6cc351f 100644
--- a/src/RNASeq.config
+++ b/src/RNASeq.config
@@ -12,6 +12,13 @@ profiles {
withName: fasta_from_bed {
container = "bedtools:2.25.0"
}
+ withName: index_fasta {
+ container = "kallisto:0.44.0"
+ }
+ withName: mapping_fastq {
+ container = "kallisto:0.44.0"
+ }
+
}
}
psmn {
@@ -44,6 +51,26 @@ profiles {
time = "12h"
queue = 'monointeldeb128'
}
+ withName: index_fasta {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "Kallisto/0.44.0"
+ executor = "sge"
+ clusterOptions = "-m e -cwd -V"
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ withName: mapping_fastq {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "Kallisto/0.44.0"
+ executor = "sge"
+ clusterOptions = "-m e -cwd -V"
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
}
}
} .
diff --git a/src/RNASeq.nf b/src/RNASeq.nf
index c38f050..fe35e21 100644
--- a/src/RNASeq.nf
+++ b/src/RNASeq.nf
@@ -88,3 +88,45 @@ bedtools getfasta -name \
}
+process index_fasta {
+ tag "$fasta.baseName"
+ cpus 4
+ publishDir "results/mapping/index/", mode: 'copy'
+
+ input:
+ file fasta from fasta_file_extracted
+
+ output:
+ file "*.index*" into index_files
+ file "*_kallisto_report.txt" into index_files_report
+
+ script:
+"""
+kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
+2> ${fasta.baseName}_kallisto_report.txt
+"""
+}
+
+process mapping_fastq {
+ tag "$reads"
+ cpus 4
+ publishDir "results/mapping/quantification/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files_trim
+ file index from index_files.collect()
+
+ output:
+ file "*" into counts_files
+
+ script:
+"""
+mkdir ${pair_id}
+kallisto quant -i ${index} -t ${task.cpus} \
+--bias --bootstrap-samples 100 -o ${pair_id} \
+${reads[0]} ${reads[1]} &> ${pair_id}/kallisto_report.txt
+"""
+}
+
+
+
--
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