From 4faeddc4beb1a2accac31b71b889c3b87057311b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 5 Aug 2020 13:35:09 -0500
Subject: [PATCH] Remove dummy fastqc
---
workflow/rna-seq.nf | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 34b5a6d..1871139 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -910,8 +910,7 @@ process fastqc {
# run fastqc
echo -e "LOG: running fastq on raw fastqs" >> ${repRID}.fastqc.log
- #fastqc *.fastq.gz -o .
- touch test_fastqc.zip
+ fastqc *.fastq.gz -o .
"""
}
@@ -1021,7 +1020,7 @@ process aggrQC {
echo -e "LOG: creating metadata table" >> ${repRID}.aggrQC.log
echo -e "Source\tSpecies\tEnds\tStranded\tSpike-in\tAssigned Reads\tRead Length\tTIN" > metadata.tsv
echo -e "Infered\t${speciesI}\t${endsI}\t${strandedI}\t${spikeI}\t-\t-\t-" >> metadata.tsv
- echo -e "Submitter\t${speciesM}\t${endsM}\t${strandedM}\t${spikeM}\t${readLengthM}\t-\t-" >> metadata.tsv
+ echo -e "Submitter\t${speciesM}\t${endsM}\t${strandedM}\t${spikeM}\t-\t${readLengthM}\t-" >> metadata.tsv
echo -e "Measured\t-\t${endsManual}\t-\t-\t${assignedReadsI}\t${readLengthI}\t${tinMedI}" >> metadata.tsv
# remove inner distance report if it is empty (SE repRID)
--
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