diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 3aa985299c6762e2ed55357f4e082ced66473167..5667086524087f106afea8e8ef5b5db64b4a0fd0 100644 --- a/.gitlab-ci.yml +++ b/.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}_${baseVar}.sif git tag --sort=-committerdate -l *.*.* | head -1) - mkdir -p ./badges/env - curl --request GET https://img.shields.io/badge/Envronment%3A%20AWS-inactive-critical?style=flat > ./badges/env/aws.svg - module load awscli/1.11.139 diff --git a/docs/nxf_aws-ci-test.json b/docs/nxf_aws-ci-test.json index 1de31087dd7fbaa917ec79c1dcda43f92899a6b9..373f8903baa747733f25cdb2f8f513720135dda1 100644 --- a/docs/nxf_aws-ci-test.json +++ b/docs/nxf_aws-ci-test.json @@ -1 +1 @@ -["utsw-bicf/gudmap_rbk.rna-seq","-r","${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"] diff --git a/docs/nxf_dnanexus-ci-test.json b/docs/nxf_dnanexus-ci-test.json index e4dde61dc430803f11cb5266b83ab66d92f3f720..88c5734247defefd2b5fa6bddaff38ba579ff065 100644 --- a/docs/nxf_dnanexus-ci-test.json +++ b/docs/nxf_dnanexus-ci-test.json @@ -1,5 +1,5 @@ { - "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" }