Test for pytest for parseMetadata: supposed to pass #54

.gitlab-ci.yml

@@ -121,7 +121,8 @@ dataQC:
   stage: unit
   script:
   - echo -e  "geneID\tchrom\ttx_start\ttx_end\tTIN" > Q-Y5F6_1M.se.sorted.deduped.tin.xls
-
+  - for i in {"chr8","chr4","chrY"}; do
+    echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"; done | singularity run 'docker://bicf/rseqc3.0:2.0.1_indev' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
   - pytest -m dataQC
 
 

workflow/tests/test_parseMetadata.py

@@ -16,7 +16,7 @@ def test_parseMetadata():
 def readLine(fileName):
     data = False
     file = open(fileName, "r")
-    if file.readline() == "uk,se,unstranded,no,Homo sapiens,Experiment_RID,Study_RID,Replicate_RID":
+    if file.readline()[] == "uk,se,unstranded,no,Homo sapiens,Experiment_RID,Study_RID,Replicate_RID":
         data = True
 
     return data