From ea8a2c38fae279b51326eecba607f32f513960aa Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 13 May 2020 16:39:10 -0500
Subject: [PATCH] Stage experiment settings as ExperimentSettings.csv to
prevent bash error
---
workflow/rna-seq.nf | 22 +++++++++++-----------
1 file changed, 11 insertions(+), 11 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 8b6166a..143b342 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -171,9 +171,9 @@ process parseMetadata {
input:
path script_parseMeta
- path fileMeta
- path experimentSettingsMeta
- path experimentMeta
+ path file from fileMeta
+ path experimentSettings, stageAs: "ExperimentSettings.csv" from experimentSettingsMeta
+ path experiment from experimentMeta
output:
path "design.csv" into metadata
@@ -184,35 +184,35 @@ process parseMetadata {
ulimit -a >> ${repRID}.parseMetadata.log
# check replicate RID metadata
- rep=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p repRID)
+ rep=\$(python3 ${script_parseMeta} -r ${repRID} -m "${file}" -p repRID)
echo -e "LOG: replicate RID metadata parsed: \${rep}" >> ${repRID}.parseMetadata.log
# get experiment RID metadata
- exp=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p expRID)
+ exp=\$(python3 ${script_parseMeta} -r ${repRID} -m "${file}" -p expRID)
echo -e "LOG: experiment RID metadata parsed: \${exp}" >> ${repRID}.parseMetadata.log
# get study RID metadata
- study=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p studyRID)
+ study=\$(python3 ${script_parseMeta} -r ${repRID} -m "${file}" -p studyRID)
echo -e "LOG: study RID metadata parsed: \${study}" >> ${repRID}.parseMetadata.log
# get endedness metadata
- endsMeta=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p endsMeta)
+ endsMeta=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p endsMeta)
echo -e "LOG: endedness metadata parsed: \${endsMeta}" >> ${repRID}.parseMetadata.log
# ganually get endness
- endsManual=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p endsManual)
+ endsManual=\$(python3 ${script_parseMeta} -r ${repRID} -m "${file}" -p endsManual)
echo -e "LOG: endedness manually detected: \${endsManual}" >> ${repRID}.parseMetadata.log
# get strandedness metadata
- stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded)
+ stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p stranded)
echo -e "LOG: strandedness metadata parsed: \${stranded}" >> ${repRID}.parseMetadata.log
# get spike-in metadata
- spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p spike)
+ spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p spike)
echo -e "LOG: spike-in metadata parsed: \${spike}" >> ${repRID}.parseMetadata.log
# get species metadata
- species=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentMeta}" -p species)
+ species=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experiment}" -p species)
echo -e "LOG: species metadata parsed: \${species}" >> ${repRID}.parseMetadata.log
# gave design file
--
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