Merge branch '19-ci.integration.test' into 'develop'

Resolve "Add integration CI test"

Closes #19

See merge request !10

.gitlab-ci.yml

@@ -2,12 +2,14 @@ before_script:
   - module add  python/3.6.1-2-anaconda
   - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
   - module load singularity/3.0.2
+  - module load nextflow/19.09.0
   - ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/* ./test_data/
   - mkdir -p ~/.deriva
   - mkdir -p ~/.bdbag
 
 stages:
   - unit
+  - integration
 
 getBag:
   stage: unit
@@ -36,4 +38,14 @@ trimData_pe:
   script:
   - if [ `nproc` -gt 8 ]; then ncore=8; else ncore=`nproc`; fi
   - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA -j ${ncore} ./test_data/fastq/Q-Y5JA.R1.fastq.gz ./test_data/fastq/Q-Y5JA.R2.fastq.gz
-  - pytest -m trimData_pe
\ No newline at end of file
+  - pytest -m trimData_pe
+
+integration_se:
+  stage: integration
+  script:
+  - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4
+
+integration_pe:
+  stage: integration
+  script:
+  - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA
\ No newline at end of file

workflow/conf/biohpc.config

@@ -15,4 +15,15 @@ process {
     container = 'docker://bicf/trimgalore:1.1'
     queue = '256GB,256GBv1,384GB'
   }
+}
+
+singularity {
+  enabled = true
+  cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
+}
+
+env {
+  http_proxy = 'http://proxy.swmed.edu:3128'
+  https_proxy = 'http://proxy.swmed.edu:3128'
+  all_proxy = 'http://proxy.swmed.edu:3128'
 }
\ No newline at end of file

workflow/rna-seq.nf

@@ -50,6 +50,7 @@ process getBag {
     """
     hostname >>${repRID_getBag}.getBag.err
     ulimit -a >>${repRID_getBag}.getBag.err
+    export https_proxy=\${http_proxy}
     ln -sf `readlink -e credential.json` ~/.deriva/credential.json 2>>${repRID_getBag}.getBag.err
     echo "LOG: deriva credentials linked" >>${repRID_getBag}.getBag.err
     deriva-download-cli dev.gudmap.org --catalog 2 ${derivaConfig} . rid=${repRID_getBag} 2>>${repRID_getBag}.getBag.err