From f6c9944abb05de8ccfa0192237f6feb2dee87b09 Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Wed, 22 Jan 2020 10:40:06 -0600
Subject: [PATCH] Reverted to ensure that Trim step is functional.
---
workflow/rna-seq.nf | 27 ++++++++++++++++-----------
1 file changed, 16 insertions(+), 11 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 7bf4db4..b769cd9 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -22,8 +22,8 @@ logsDir = "${outDir}/Logs"
derivaConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json")
// Define script files
-script_bdbagFetch = file ("${baseDir}/scripts/bdbagFetch.sh")
-script_parseMeta = file ("${baseDir}/scripts/parseMeta.py")
+script_bdbagFetch = Channel.fromPath("${baseDir}/scripts/bdbagFetch.sh")
+script_parseMeta = Channel.fromPath("${baseDir}/scripts/parseMeta.py")
/*
* splitData: split bdbag files by replicate so fetch can occure in parallel, and rename files to replicate rid
@@ -156,6 +156,7 @@ endsManual = Channel.create()
stranded = Channel.create()
spike = Channel.create()
species = Channel.create()
+reference = Channel.create()
metadata.splitCsv(sep: ',', header: false).separate(
rep,
endsMeta,
@@ -180,20 +181,23 @@ if (species == "") {
exit 1
}
+spike.subscribe { println "$it"}
+
// Setting references
-if (spike) {
+if (spike == 'yes') {
if (species == "Homo sapiens") {
- reference = file ("/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12-S/hisat2")
+ reference = Channel.fromPath ("/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12-S/hisat2")
} else if (species == "Mus musculus") {
- reference = file ("/project/BICF/BICF_Core/shared/gudmap/references/GRCm38.P6-S/hisat2")
+ reference = Channel.fromPath ("/project/BICF/BICF_Core/shared/gudmap/references/GRCm38.P6-S/hisat2")
}
} else {
if (species == "Homo sapiens") {
- reference = file ("/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2")
+ reference = Channel.fromPath ("/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2")
} else if (species == "Mus musculus") {
- reference = file ("/project/BICF/BICF_Core/shared/gudmap/references/GRCm38.P6/hisat2")
+ reference = Channel.fromPath ("/project/BICF/BICF_Core/shared/gudmap/references/GRCm38.P6/hisat2")
}
}
+reference.subscribe { println "$it }
/*
* trimData: trims any adapter or non-host sequences from the data
@@ -237,6 +241,7 @@ process alignReads {
val endsManual_alignReads
val stranded_alignReads
path fqs from fastqs_trimmed
+ val reference
output:
set repRID, file ("${repRID}.unal.gz"), file ("${repRID}.bam"), file ("${repRID}.bai")
@@ -244,10 +249,10 @@ process alignReads {
script:
"""
if [ "${endsManual_alignReads}" == 'pe' ]; then
- hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x ${reference}/genome -1 ${fqs[0]} -2 ${fqs[1]} 1>${repRID}.align.out 2> ${repRID}.align.err;
- else hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x ${reference}/genome -U ${fqs[0]} 1>${repRID}.align.out 2> ${repRID}.align.err;
+ hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x ${reference}/genome -1 ${fqs[0]} -2 ${fqs[1]} 1>${repRID}.align.out 2>${repRID}.align.err;
+ else hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x ${reference}/genome -U ${fqs[0]} 1>${repRID}.align.out 2>${repRID}.align.err;
fi;
- samtools view -1 --threads `nproc` -o ${repRID}.bam ${repRID}.sam 1>${repRID}.align.out 2> ${repRID}.align.err;
- samtools sort -@ `nproc` -O BAM ${repRID}.bam 1>${repRID}.align.out 2> ${repRID}.align.err;
+ samtools view -1 --threads `nproc` -o ${repRID}.bam ${repRID}.sam 1>>${repRID}.align.out 2>>${repRID}.align.err;
+ samtools sort -@ `nproc` -O BAM -o ${repRID}.bam 1>>${repRID}.align.out 2>>${repRID}.align.err;
"""
}
--
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