From fbd2da78f697d4c0d59c2f9e92fd307e309fa0e6 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 19 Jan 2020 01:23:51 -0600
Subject: [PATCH] Fix len fastqs
---
workflow/rna-seq.nf | 3 ++-
workflow/scripts/parseMeta.py | 6 +++---
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index e0b6cd3..b8de5d8 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -115,8 +115,9 @@ process parseMetadata {
path experimentMeta
output:
- val ends
+ val endsMeta
val endsManual
+ val ends
val stranded
val spike
val specie
diff --git a/workflow/scripts/parseMeta.py b/workflow/scripts/parseMeta.py
index d2fb8fa..825a379 100644
--- a/workflow/scripts/parseMeta.py
+++ b/workflow/scripts/parseMeta.py
@@ -25,7 +25,7 @@ def main():
else:
rep=metaFile["Replicate_RID"].unique()[0]
print(rep)
- if (len(metaFile[metaFile["File_Type"] == "FastQ"]) > 2):
+ if (len(metaFile[metaFile["File_Type"] == "FastQ"].all()) > 2):
print("There are more then 2 fastq's in the metadata: " + " ".join(metaFile[metaFile["File_Type"] == "FastQ"].RID))
exit(1)
if (args.parameter == "ends"):
@@ -37,9 +37,9 @@ def main():
ends = "uk"
print(ends)
if (args.parameter == "endsManual"):
- if (len(metaFile[metaFile["File_Type"] == "FastQ"]) == 1):
+ if (len(metaFile[metaFile["File_Type"] == "FastQ"].all()) == 1):
endsManual = "se"
- elif (len(metaFile[metaFile["File_Type"] == "FastQ"]) == 2):
+ elif (len(metaFile[metaFile["File_Type"] == "FastQ"].all()) == 2):
endsManual = "pe"
print(endsManual)
if (args.parameter == "stranded"):
--
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