From d92d93f967a920462769bfc282a7eb632c15543b Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Wed, 22 Jan 2020 10:56:52 -0600
Subject: [PATCH] Updated Hisat2 options, and output of parseMeta.
---
workflow/rna-seq.nf | 6 +++---
workflow/scripts/parseMeta.py | 9 ++++++---
2 files changed, 9 insertions(+), 6 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index a96eaf6..4df8b08 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -197,7 +197,7 @@ if (spike == 'yes') {
reference = Channel.fromPath ("/project/BICF/BICF_Core/shared/gudmap/references/GRCm38.P6/hisat2")
}
}
-reference.subscribe { println "$it" }
+//reference.subscribe { println "$it" }
/*
* trimData: trims any adapter or non-host sequences from the data
@@ -249,8 +249,8 @@ 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 ${stranded_alignReads} -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 ${stranded_alignReads} -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 -o ${repRID}.bam 1>>${repRID}.align.out 2>>${repRID}.align.err;
diff --git a/workflow/scripts/parseMeta.py b/workflow/scripts/parseMeta.py
index 43ca239..f669cfa 100644
--- a/workflow/scripts/parseMeta.py
+++ b/workflow/scripts/parseMeta.py
@@ -54,9 +54,12 @@ def main():
# Get strandedness metadata from 'Experiment Settings.csv'
if (args.parameter == "stranded"):
if (metaFile.Has_Strand_Specific_Information.unique() == "yes"):
- stranded = "stranded"
+ if endsManual == "se":
+ stranded = "--rna-strandness F"
+ else:
+ stranded = "--rna-strandness FR"
elif (metaFile.Has_Strand_Specific_Information.unique() == "no"):
- stranded = "unstranded"
+ stranded = ""
else:
print("Stranded metadata not match expected options: " + metaFile.Has_Strand_Specific_Information.unique())
exit(1)
@@ -85,4 +88,4 @@ def main():
print(species)
if __name__ == '__main__':
- main()
\ No newline at end of file
+ main()
--
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