From a697e78be65a2b09eddc852322354ff92da00d1c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 1 May 2020 23:35:58 -0500
Subject: [PATCH] Fix SE downsample output optional
---
workflow/rna-seq.nf | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 52e5d61..917f199 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -354,7 +354,7 @@ process downsampleData {
output:
path ("sampled.1.fq") into fastqs1Sample
- path ("sampled.2.fq") optional true into fastqs2Sample
+ path ("sampled.2.fq") into fastqs2Sample
path ("${repRID}.downsampleData.{out,err}")
script:
@@ -367,6 +367,7 @@ process downsampleData {
then
echo "LOG: downsampling single-end trimmed fastq" >> ${repRID}.downsampleData.err
seqtk sample -s100 *trimmed.fq.gz 100000 1> sampled.1.fq 2>> ${repRID}.downsampleData.err
+ touch sampled.2.fq
elif [ "${ends}" == "pe" ]
then
echo "LOG: downsampling read 1 of paired-end trimmed fastq" >> ${repRID}.downsampleData.err
--
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