Use updated input bag name

.gitlab-ci.yml

@@ -50,7 +50,7 @@ getData:
   - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag --version > version_bdbag.txt
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - unzip ./test_data/bag/staging/Q-Y5F6_inputBag_20201228.zip
-  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6_inputBag_20201228 Q-Y5F6 TEST
+  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6_inputBag Q-Y5F6 TEST
   - pytest -m getData
   artifacts:
     name: "$CI_JOB_NAME"

workflow/rna-seq.nf

@@ -241,7 +241,7 @@ process getData {
 
     # bag fetch fastq's only and rename by repRID
     echo -e "LOG: fetching replicate bdbag" >> ${repRID}.getData.log
-    sh ${script_bdbagFetch} \${replicate} ${repRID}
+    sh ${script_bdbagFetch} \${replicate::-9} ${repRID}
     echo -e "LOG: fetched" >> ${repRID}.getData.log
     """
 }