From 131b55174bb860a1c0284b16e0cf8fc502625afe Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 18 Jan 2020 16:31:32 -0600
Subject: [PATCH] Make .nf scripts more readable
---
workflow/rna-seq.nf | 17 +++++++++++++++++
1 file changed, 17 insertions(+)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 55be645..d4b917f 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -46,8 +46,12 @@ process getBag {
hostname >>${repRID}.getBag.err
ulimit -a >>${repRID}.getBag.err
export https_proxy=\${http_proxy}
+
+ # link credential file for authentication
ln -sf `readlink -e credential.json` ~/.deriva/credential.json 2>>${repRID}.getBag.err
echo "LOG: deriva credentials linked" >>${repRID}.getBag.err
+
+ # deriva-download replicate RID
deriva-download-cli dev.gudmap.org --catalog 2 ${derivaConfig} . rid=${repRID} 2>>${repRID}.getBag.err
"""
}
@@ -77,12 +81,20 @@ process getData {
hostname >>${repRID}.getData.err
ulimit -a >>${repRID}.getData.err
export https_proxy=\${http_proxy}
+
+ # link deriva cookie for authentication
ln -sf `readlink -e deriva-cookies.txt` ~/.bdbag/deriva-cookies.txt >>${repRID}.getData.err
echo "LOG: deriva cookie linked" >>${repRID}.getData.err
+
+ # get bagit basename
replicate=\$(basename "${bagit}" | cut -d '.' -f1)
echo "LOG: \${replicate}" >>${repRID}.getData.err
+
+ # unzip bagit
unzip ${bagit} 2>>${repRID}.getData.err
echo "LOG: replicate bdbag unzipped" >>${repRID}.getData.err
+
+ # bagit fetch fastq's only and rename by repRID
sh bdbagFetch.sh \${replicate} ${repRID} 2>>${repRID}.getData.err
echo "LOG: replicate bdbag fetched" >>${repRID}.getData.err
"""
@@ -106,12 +118,17 @@ process trimData {
script:
"""
+ hostname >>${repRID}.trimData.err
+ ulimit -a >>${repRID}.trimData.err
+
if [ `nproc` -gt 8 ]
then
ncore=8
else
ncore=`nproc`
fi
+
+ # trim fastqs
if [ '${fastq[1]}' == 'null' ]
then
ends='se'
--
GitLab