Merge branch 'master' into 'develop'

Hardwire pipeline version for env tests

See merge request !80

.gitlab-ci.yml

@@ -1041,10 +1041,6 @@ dnanexus:
   script:
     - hostname
     - ulimit -a
-    - baseImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep gudmap-rbk_base | cut -d"/" -f2 | cut -d":" -f1)
-    - baseVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep gudmap-rbk_base | cut -d"/" -f2 | cut -d":" -f2)
-    - echo ${dir}${baseImg}_${baseVar}.sif
-    - latest_release_tag=$(singularity run ${dir}${baseImg}_${baseVar}.sif git tag --sort=-committerdate -l *.*.* | head -1)
     - mkdir -p ./badges/env
     - curl --request GET https://img.shields.io/badge/Envronment%3A%20DNAnexus-inactive-critical?style=flat > ./badges/env/dnanexus.svg
     - module load dxtoolkit/python27/0.294.0
@@ -1089,10 +1085,6 @@ aws:
   script:
     - hostname
     - ulimit -a
-    - baseImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep gudmap-rbk_base | cut -d"/" -f2 | cut -d":" -f1)
-    - baseVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep gudmap-rbk_base | cut -d"/" -f2 | cut -d":" -f2)
-    - echo ${dir}${baseImg}_${baseVar}.sif
-    - latest_release_tag=$(singularity run ${dir}${baseImg}_${baseVar}.sif git tag --sort=-committerdate -l *.*.* | head -1)
     - mkdir -p ./badges/env
     - curl --request GET https://img.shields.io/badge/Envronment%3A%20AWS-inactive-critical?style=flat > ./badges/env/aws.svg
     - module load awscli/1.11.139

docs/nxf_aws-ci-test.json

-["utsw-bicf/gudmap_rbk.rna-seq","-r","${latest_release_tag}","-profile","aws","--deriva","s3://bicf-output/ci-env/auth/credential.json","--bdbag","s3://bicf-output/ci-env/auth/cookies.txt","--repRID","Q-Y5F6","--source","staging","--upload","false","--dev","false","--ci","true","--track","false","-with-report","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride_report.html","--refSource","datahub","--outDir","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride","--fastqsForce","s3://bicf-output/ci-env/input/*.fastq.gz"]
+["utsw-bicf/gudmap_rbk.rna-seq","-r","v2.0.0","-profile","aws","--deriva","s3://bicf-output/ci-env/auth/credential.json","--bdbag","s3://bicf-output/ci-env/auth/cookies.txt","--repRID","Q-Y5F6","--source","staging","--upload","false","--dev","false","--ci","true","--track","false","-with-report","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride_report.html","--refSource","datahub","--outDir","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride","--fastqsForce","s3://bicf-output/ci-env/input/*.fastq.gz"]

docs/nxf_dnanexus-ci-test.json

 {
-	"pipeline_url": "https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq.git -r ${latest_release_tag}",
+	"pipeline_url": "https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq.git -r v2.0.0",
 	"args": "-profile dnanexus --deriva dx://NextFlow_Prototype:/ci-env/auth/credential.json --bdbag dx://NextFlow_Prototype:/ci-env/auth/cookies.txt --repRID Q-Y5F6 --source staging --upload false --dev false --ci true --track false -with-report dx://NextFlow_Prototype:/ci-env/output/Q-Y5F6_fastqoverride_report.html --refSource datahub --outDir dx://NextFlow_Prototype:ci-env/output/Q-Y5F6_fastqoverride --fastqsForce dx://NextFlow_Prototype:/ci-env/input/*.fastq.gz",
-	"license": "${NXF_XPACK_LICENSE}"
+	"license": "$NXF_XPACK_LICENSE"
 }