From c2cdbcc2fb921ddc507f10d42ac18bb3695fb375 Mon Sep 17 00:00:00 2001
From: z483800 <109-z483800@users.noreply.gitlab.biologie.ens-lyon.fr>
Date: Fri, 17 Jan 2020 15:00:46 +0000
Subject: [PATCH] add kalliso indexing
---
src/RNAseq.config | 56 +++++++++++++++++++++++++++++++++++++++++++++++
src/RNAseq.nf | 18 +++++++++++++++
2 files changed, 74 insertions(+)
diff --git a/src/RNAseq.config b/src/RNAseq.config
index 5d949d4..a9ea266 100644
--- a/src/RNAseq.config
+++ b/src/RNAseq.config
@@ -161,3 +161,59 @@ profiles {
}
}
}
+
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withNamek index_fasta {
+ container = "lbmc/kallisto:0.44.0"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ singularity.cacheDir = "./bin/"
+ process {
+ withName: index_fasta {
+ container = "lbmc/kallisto:0.44.0"
+ cpus = 4
+ }
+ }
+ }
+ psmn{
+ process{
+ withName: index_fasta {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 16
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ }
+ }
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.cacheDir = "$baseDir/.singularity_in2p3/"
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "lbmc/kallisto:0.44.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
+}
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index e9c859d..f6633f0 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -86,3 +86,21 @@ bedtools getfasta -name \
-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
"""
}
+
+process index_fasta {
+ tag "$fasta.baseName"
+ publishDir "results/mapping/index/", mode: 'copy'
+
+ input:
+ file fasta from fasta_files_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
+"""
+}
--
GitLab