Upgrade docker images (gudmaprbkfilexfer and trimgalore) to 1.1

.gitlab-ci.yml

@@ -11,6 +11,6 @@ stages:
 unit:
   stage: unit
   script:
-  - singularity run 'docker://bicf/bdbag:1.0' bdbag --materialize ./test_data/File_Q-Y53P.zip
-  - singularity run 'docker://bicf/bdbag:1.0' bdbag --validate full ./test_data/File_Q-Y53P/
+  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' bdbag --materialize ./test_data/File_Q-Y53P.zip
+  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' bdbag --validate full ./test_data/File_Q-Y53P/
   - if [[ $(md5sum test_data/File_Q-Y53P/data/assets/Study/Q-Y4H0/Experiment/Q-Y4BY/Replicate/Q-Y5F8/hMARIS_SIX2+_RiboDep#1.gene.rpkm.txt | awk '{ print $1 }') != $(cat test_data/File_Q-Y53P/data/File.csv | cut -d ',' -f10 | tail -1) ]]; then exit 21; fi;

workflow/conf/biohpc.config

@@ -5,13 +5,13 @@ process {
 
   // Process specific configuration
   withName:splitData {
-    container = 'docker://bicf/gudmaprbkfilexfer:1.0'
+    container = 'docker://bicf/gudmaprbkfilexfer:1.1'
   }
   withName:getData {
-    container = 'docker://bicf/gudmaprbkfilexfer:1.0'
+    container = 'docker://bicf/gudmaprbkfilexfer:1.1'
   }
   withName:trimData {
-    container = 'docker://bicf/trimgalore:1.0'
+    container = 'docker://bicf/trimgalore:1.1'
     queue = '256GB,256GBv1,384GB'
   }
 }

workflow/conf/conda.env.bdbag.yml

-name: bdbag
-dependencies:
-  - pandas=0.23.3=py36_0
-  - pip:
-    - bdbag==1.5.5