From bf9d4f713314dc7d1ce8545f67a14a5b20c7f51f Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 10 Feb 2020 15:01:15 -0600
Subject: [PATCH] Fix temp comment out reference s3 bucket
---
workflow/rna-seq.nf | 23 +----------------------
1 file changed, 1 insertion(+), 22 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index fdba0c5..d68852c 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -33,7 +33,7 @@ logsDir = "${outDir}/Logs"
// Define fixed files
derivaConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json")
-#referenceBase = "s3://bicf-references"
+//referenceBase = "s3://bicf-references"
referenceBase = "/project/BICF/BICF_Core/shared/gudmap/references"
// Define script files
@@ -365,25 +365,4 @@ process fastqc {
# run fastqc
fastqc *.fastq.gz -o . >>${repRID}.fastqc.err
"""
-}
-
-/*
- *rseqc: run RSeQC to collect qc stats and infer experimental settings
-*/
-process rseqc {
- tag "${repRID}"
- publishDir "${logsDir}", mode: 'copy', pattern: "*.rseqc.err"
-
- input:
-
- output:
-
- script:
- """
- hostname >${repRID}.rseqc.err
- ulimit -a >>${repRID}.rseqc.err
-
- # run
- #infer_experiment.py -r
- """
}
\ No newline at end of file
--
GitLab