From 0acf38a4601f995408d94ff4d54f88202b3261a5 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 19 Jan 2020 00:29:24 -0600
Subject: [PATCH] Add manual detection of endness if not stored
---
workflow/rna-seq.nf | 10 ++++++++++
workflow/scripts/parseMeta.py | 8 ++++++++
2 files changed, 18 insertions(+)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 94d5eea..6170be7 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -116,6 +116,7 @@ process parseMetadata {
output:
val ends
+ val endsManual
val stranded
val spike
val specie
@@ -133,6 +134,15 @@ process parseMetadata {
ends=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p ends)
echo "LOG: endedness metadata parsed: \${ends}" >>${repRID}.parseMetadata.err
+ # Manually get endness
+ endsManual=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p endsManual)
+ echo "LOG: endedness manually detected: \${ends}" >>${repRID}.parseMetadata.err
+ if [ \${ends} == "uk" ]
+ then
+ ends=\${endsManual}
+ echo "LOG: endness metadata overwitten my manually detected" >>${repRID}.parseMetadata.err
+ fi
+
# Get strandedness metadata
stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded)
echo "LOG: strandedness metadata parsed: \${stranded}" >>${repRID}.parseMetadata.err
diff --git a/workflow/scripts/parseMeta.py b/workflow/scripts/parseMeta.py
index 0dc9056..83f4a80 100644
--- a/workflow/scripts/parseMeta.py
+++ b/workflow/scripts/parseMeta.py
@@ -33,10 +33,18 @@ def main():
ends = "se"
elif (metaFile.Paired_End.unique() == "Paired End"):
ends = "pe"
+ elif (metaFile.Paired_End.unique() == ""):
+ ends = "uk"
else:
print("Ends metadata not match expected options: " + metaFile.Paired_End.unique())
exit(1)
print(ends)
+ if (args.parameter == "endsManual"):
+ if (len(metaFile[metaFile["File_Type"] == "FastQ"]) == 1):
+ endsManual = "se"
+ elif (len(metaFile[metaFile["File_Type"] == "FastQ"]) == 2):
+ endsManual = "pe"
+ print(endsManual)
if (args.parameter == "stranded"):
if (metaFile.Has_Strand_Specific_Information.unique() == "yes"):
stranded = "stranded"
--
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