CI unit: getRef cp local, getData test version of script to fetch txt

.gitlab-ci.yml

@@ -23,7 +23,7 @@ getData:
   script:
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - unzip ./test_data/bagit/Replicate_16-1ZX4
-  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' sh ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4
+  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' sh ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4 TEST
   - pytest -m getData
 
 parseMetadata:
@@ -38,8 +38,12 @@ parseMetadata:
 getRef:
   stage: unit
   script:
-  - singularity run 'docker://bicf/awscli:1.1' aws s3 ls s3://bicf-references/mouse/0.0.1/GRCm38.P6
-  - singularity run 'docker://bicf/awscli:1.1' aws s3 ls s3://bicf-references/human/0.0.1/GRCh38.p12
+  - #singularity run 'docker://bicf/awscli:1.1' aws s3 ls s3://bicf-references/mouse/0.0.1/GRCm38.P6
+  - #singularity run 'docker://bicf/awscli:1.1' aws s3 ls s3://bicf-references/human/0.0.1/GRCh38.p12
+  - mkdir -p hu
+  - mkdir -p mo
+  - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./hu/
+  - cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./mo/
 
 trimData:
   stage: unit

workflow/scripts/bdbagFetch.sh

 #!/bin/bash
 
-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.\.fastq\.gz");
-    mv ${i} ./${path}
-done;
\ No newline at end of file
+if [ ! -z ${3}} ]
+then
+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.\.fastq\.gz")
+        mv ${i} ./${path}
+    done
+elif [ ${3} == "TEST" ]
+then
+    bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1}
+fi
\ No newline at end of file