From 829a61870ffee62aaff7f7beec4238732deb200b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 28 Dec 2020 13:09:38 -0600
Subject: [PATCH] Update naming convention in dataQC
---
workflow/rna-seq.nf | 8 ++++----
workflow/scripts/tinHist.py | 6 +++---
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 94ad34a..1f0a4b2 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1133,8 +1133,8 @@ process dataQC {
val ends from endsInfer_dataQC
output:
- path "${repRID}.tin.hist.tsv" into tinHist
- path "${repRID}.tin.med.csv" into tinMedInfer_fl
+ path "${repRID}_tin.hist.tsv" into tinHist
+ path "${repRID}_tin.med.csv" into tinMedInfer_fl
path "${repRID}.insertSize.inner_distance_freq.txt" into innerDistance
script:
@@ -1157,12 +1157,12 @@ process dataQC {
if [ "${ends}" == "pe" ]
then
echo -e "LOG: calculating inner distances for ${ends}" >> ${repRID}.dataQC.log
- inner_distance.py -i "${bam}" -o ${repRID}.insertSize -r ./bed/genome.bed
+ inner_distance.py -i "${bam}" -o ${repRID}_insertSize -r ./bed/genome.bed
echo -e "LOG: calculated" >> ${repRID}.dataQC.log
elif [ "${ends}" == "se" ]
then
echo -e "LOG: creating dummy inner distance file for ${ends}" >> ${repRID}.dataQC.log
- touch ${repRID}.insertSize.inner_distance_freq.txt
+ touch ${repRID}_insertSize.inner_distance_freq.txt
fi
"""
}
diff --git a/workflow/scripts/tinHist.py b/workflow/scripts/tinHist.py
index a95a9c2..ee36bb6 100644
--- a/workflow/scripts/tinHist.py
+++ b/workflow/scripts/tinHist.py
@@ -17,7 +17,7 @@ def get_args():
def main():
args = get_args()
- tin = pd.read_csv(args.repRID + '.sorted.deduped.tin.xls',
+ tin = pd.read_csv(args.repRID + '_sorted.deduped.tin.xls',
sep="\t", header=0)
hist = pd.cut(tin['TIN'], bins=pd.interval_range(
@@ -42,8 +42,8 @@ def main():
hist = hist[['TOTAL'] + [i for i in hist.columns if i != 'TOTAL']]
hist = hist.T.fillna(0.0).astype(int)
#hist = hist.apply(lambda x: x/x.sum()*100, axis=1)
- hist.to_csv(args.repRID + '.tin.hist.tsv', sep='\t')
- medFile = open(args.repRID + '.tin.med.csv', "w")
+ hist.to_csv(args.repRID + '_tin.hist.tsv', sep='\t')
+ medFile = open(args.repRID + '_tin.med.csv', "w")
medFile.write(str(round(tin['TIN'][(tin['TIN'] != 0)].median(), 2)))
medFile.close()
--
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