Use updated input bag name

.gitlab-ci.yml

@@ -49,8 +49,8 @@ getData:
   script:
   - 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.zip
-  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6 Q-Y5F6 TEST
+  - 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
   - pytest -m getData
   artifacts:
     name: "$CI_JOB_NAME"
@@ -655,7 +655,7 @@ override_inputBag:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --inputBagForce ./test_data/bag/staging/Replicate_Q-Y5F6.zip --upload false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --inputBagForce ./test_data/bag/staging/Q-Y5F6_inputBag_20201228.zip --upload false --ci true
   - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"

workflow/rna-seq.nf

@@ -231,7 +231,7 @@ process getData {
     echo -e "LOG: linked" >> ${repRID}.getData.log
 
     # get bag basename
-    replicate=\$(basename "${inputBag}" | cut -d "_" -f1)
+    replicate=\$(basename "${inputBag}")
     echo -e "LOG: bag replicate name \${replicate}" >> ${repRID}.getData.log
 
     # unzip bag

workflow/scripts/bdbagFetch.sh

@@ -2,7 +2,7 @@
 
 if [ -z "${3}" ]
 then
-    bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}_inputBag
+    bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
     for i in $(find */ -name "*R*.fastq.gz")
     do
         path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz")
@@ -10,5 +10,5 @@ then
     done
 elif [ "${3}" == "TEST" ]
 then
-    bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1}_inputBag
+    bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1}
 fi