From 9662650248b1e630a8d9a6457158cbeeefb81e7b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 18 Jan 2020 23:33:10 -0600
Subject: [PATCH] Fix script as input for parseMetadata
---
workflow/rna-seq.nf | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 61f3318..9fd7ed7 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -95,7 +95,7 @@ process getData {
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
+ sh ${script_bdbagFetch} \${replicate} ${repRID} 2>>${repRID}.getData.err
echo "LOG: replicate bdbag fetched" >>${repRID}.getData.err
"""
}
@@ -108,7 +108,7 @@ process parseMetadata {
publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.parseMetadata.err"
input:
- path pscript_arseMeta
+ path script_parseMeta
val repRID
path fileMeta
path experimentSettingsMeta
@@ -126,23 +126,23 @@ process parseMetadata {
ulimit -a >>${repRID}.parseMetadata.err
# Check replicate RID metadata
- rep=\$(python3 ${baseDir}/scripts/parseMeta.py -r ${repRID} -m "${fileMeta}" -p repRID)
+ rep=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p repRID)
echo "LOG: replicate RID metadata parsed: \${rep}" >>${repRID}.parseMetadata.err
# Get endedness metadata
- ends=\$(python3 ${baseDir}/scripts/parseMeta.py -r ${repRID} -m "${experimentSettingsMeta}" -p ends)
+ ends=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p ends)
echo "LOG: endedness metadata parsed: \${ends}" >>${repRID}.parseMetadata.err
# Get strandedness metadata
- stranded=\$(python3 ${baseDir}/scripts/parseMeta.py -r ${repRID} -m "${experimentSettingsMeta}" -p stranded)
+ stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded)
echo "LOG: strandedness metadata parsed: \${stranded}" >>${repRID}.parseMetadata.err
# Get spike-in metadata
- spike=\$(python3 ${baseDir}/scripts/parseMeta.py -r ${repRID} -m "${experimentSettingsMeta}" -p spike)
+ spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p spike)
echo "LOG: spike-in metadata parsed: \${spike}" >>${repRID}.parseMetadata.err
# Get species metadata
- specie=\$(python3 ${baseDir}/scripts/parseMeta.py -r ${repRID} -m "${experimentMeta}" -p specie)
+ specie=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentMeta}" -p specie)
echo "LOG: species metadata parsed: \${specie}" >>${repRID}.parseMetadata.err
"""
}
--
GitLab