diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 87348e65a26ec0fdfa75a0d60febe6e755cb26f0..da81becce22ae6a06ae0419b5770b87a1039dee9 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1047,6 +1047,7 @@ dnanexus: - export NXF_XPACK_LICENSE=${nxf_license} - dx upload ./test_data/auth/c* --path /ci-env/auth/ --parents --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} - dx upload ./test_data/fastq/xsmall/Q-Y5F6_10K.R{1,2}.fastq.gz --path /ci-env/input/ --parents --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} + - latest_release_tag=$(git tag --sort=-committerdate -l *.*.* | head -1) - > dx run nf-dxapp-bicf --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} \ --delay-workspace-destruction \ @@ -1093,6 +1094,7 @@ aws: - aws configure set region ${aws_region} - aws s3 cp ./test_data/auth/ s3://bicf-output/ci-env/auth/ --exclude "*" --include "c*" --recursive - aws s3 cp ./test_data/fastq/xsmall/ s3://bicf-output/ci-env/input/ --exclude "*" --include "Q-Y5F6_10K.R*.fastq.gz" --recursive + - latest_release_tag=$(git tag --sort=-committerdate -l *.*.* | head -1) - > id=$(aws batch submit-job\ --job-name nf-GUDMAP_RBK_ci-env\ diff --git a/CHANGELOG.md b/CHANGELOG.md index 36020f0d0050b198f7c888891489e5c656bba893..f11168501c90b6c80d9b0c2bc51d44480896c9a0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -# v2.0.0rc02 +# v2.0.0 **User Facing** * Endness metadata "Single Read" changed to "Single End" in data-hub, pipeline updated to handle (#110) ("Single Read" still acceptable for backwards compatibility) * Strandedness metadata "yes"/"no" changed to boolean "t"/"f" in data-hub, pipeline updated to handle (#70) ("yes"/"no" still acceptable for backwards compatibility) diff --git a/docs/nxf_aws-ci-test.json b/docs/nxf_aws-ci-test.json index de8752b202a05d6ed8f6aea2e1eed845917fcb7d..1de31087dd7fbaa917ec79c1dcda43f92899a6b9 100644 --- a/docs/nxf_aws-ci-test.json +++ b/docs/nxf_aws-ci-test.json @@ -1 +1 @@ -["utsw-bicf/gudmap_rbk.rna-seq","-r","env.ci","-profile","aws","--deriva","s3://bicf-output/ci-env/auth/credential.json","--bdbag","s3://bicf-output/ci-env/auth/cookies.txt","--repRID","Q-Y5F6","--source","staging","--upload","false","--dev","false","--ci","true","--track","false","-with-report","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride_report.html","--refSource","datahub","--outDir","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride","--fastqsForce","s3://bicf-output/ci-env/input/*.fastq.gz"] +["utsw-bicf/gudmap_rbk.rna-seq","-r","${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"] diff --git a/docs/nxf_dnanexus-ci-test.json b/docs/nxf_dnanexus-ci-test.json index cb523c7244600f516543012c962b4fd3b60d777f..e4dde61dc430803f11cb5266b83ab66d92f3f720 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 env.ci", + "pipeline_url": "https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq.git -r ${latest_release_tag}", "args": "-profile dnanexus --deriva dx://NextFlow_Prototype:/ci-env/auth/credential.json --bdbag dx://NextFlow_Prototype:/ci-env/auth/cookies.txt --repRID Q-Y5F6 --source staging --upload false --dev false --ci true --track false -with-report dx://NextFlow_Prototype:/ci-env/output/Q-Y5F6_fastqoverride_report.html --refSource datahub --outDir dx://NextFlow_Prototype:ci-env/output/Q-Y5F6_fastqoverride --fastqsForce dx://NextFlow_Prototype:/ci-env/input/*.fastq.gz", - "license": "$NXF_XPACK_LICENSE" + "license": "${NXF_XPACK_LICENSE}" }