From 4ca7cd19546c0c6000e1cffa5d3d94fec5682712 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 3 Feb 2020 22:10:57 -0600
Subject: [PATCH] Fix outdir for fastqc ci and process
---
.gitlab-ci.yml | 2 +-
workflow/rna-seq.nf | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5a4263a..10b06f9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -70,7 +70,7 @@ dedupData:
fastqc:
stage: unit
script:
- - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz .
+ - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz -o .
- pytest -m fastqc
integration_se:
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 3cb62a5..0fd3ee0 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -354,6 +354,6 @@ process fastqc {
ulimit -a >>${repRID}.fastqc.err
# run fastqc
- fastqc *.fastq.gz >>${repRID}.fastqc.err
+ fastqc *.fastq.gz -o . >>${repRID}.fastqc.err
"""
}
\ No newline at end of file
--
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