From b949a3b0f9b7f767e16fc26afc63953433cd8912 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 3 Aug 2020 14:33:11 -0500
Subject: [PATCH] Convert num read length to str in bash
---
.gitlab-ci.yml | 3 ++-
workflow/rna-seq.nf | 1 +
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 29f4925..659eadf 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -39,7 +39,8 @@ parseMetadata:
- spike=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike)
- species=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species)
- readLength=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.stageNew.csv" -p readLength)
- - echo -e "${endsMeta},${endsManual},${stranded},${spike},${species},${readLength},${exp},${study},${rep}" > design.csv
+ - readLength=""${readLength}
+ echo -e "${endsMeta},${endsManual},${stranded},${spike},${species},${readLength},${exp},${study},${rep}" > design.csv
- pytest -m parseMetadata
inferMetadata:
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 1443869..9b77129 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -239,6 +239,7 @@ process parseMetadata {
# get read length metadata
readLength=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experiment}" -p readLength)
+ readLength=""\${readLength}
echo -e "LOG: read length metadata parsed: \${readLength}" >> ${repRID}.parseMetadata.log
# gave design file
--
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