Convert num read length to str in bash

.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:

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