diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 777081d0c657a6de68b2731ecb021ae865170654..14426c66432381603b332f05c340e0a7591c4cf4 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1091,13 +1091,13 @@ aws: - export AWS_ACCESS_KEY_ID=${aws_accesskeyid} - export AWS_SECRET_ACCESS_KEY=${aws_secretaccesskey} - aws configure set region ${aws_region} - - aws s3 cp ./test_data/auth/ s3://bicf-output/ci-env/auth/ --exclude "*" --include "c*" --recursive - - aws s3 cp ./test_data/fastq/xsmall/ s3://bicf-output/ci-env/input/ --exclude "*" --include "Q-Y5F6_10K.R*.fastq.gz" --recursive + - aws s3 cp ./test_data/auth/ s3://bicf-nf-output/ci-env/auth/ --exclude "*" --include "c*" --recursive + - aws s3 cp ./test_data/fastq/xsmall/ s3://bicf-nf-output/ci-env/input/ --exclude "*" --include "Q-Y5F6_10K.R*.fastq.gz" --recursive - > id=$(aws batch submit-job\ --job-name nf-GUDMAP_RBK_ci-env\ - --job-queue priority-bicf\ - --job-definition nextflow-bicf-nextflow\ + --job-queue default-bicf\ + --job-definition nextflow-nf\ --container-overrides command=$(envsubst < ./docs/nxf_aws-ci-test.json)) id=$(echo ${id}| grep -oP "jobId\K.*" | tr -d '"' | tr -d ":" | tr -d " " | tr -d "}") - > @@ -1121,8 +1121,8 @@ aws: - export AWS_ACCESS_KEY_ID=${aws_accesskeyid} - export AWS_SECRET_ACCESS_KEY=${aws_secretaccesskey} - aws configure set region ${aws_region} - - aws s3 rm s3://bicf-output/ci-env/auth/ --recursive - - aws s3 rm s3://bicf-output/ci-env/input/ --recursive + - aws s3 rm s3://bicf-nf-output/ci-env/auth/ --recursive + - aws s3 rm s3://bicf-nf-output/ci-env/input/ --recursive artifacts: when: always paths: diff --git a/docs/nxf_aws-ci-test.json b/docs/nxf_aws-ci-test.json index 580c84529c672dc3e658baecfd9ae7fd72a4678e..f802db67c8c35a30f3b87a37a5501b1beb4e704c 100644 --- a/docs/nxf_aws-ci-test.json +++ b/docs/nxf_aws-ci-test.json @@ -1 +1 @@ -["utsw-bicf/gudmap_rbk.rna-seq","-r","develop","-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","--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","develop","-profile","aws","--deriva","s3://bicf-nf-output/ci-env/auth/credential.json","--bdbag","s3://bicf-nf-output/ci-env/auth/cookies.txt","--repRID","Q-Y5F6","--source","staging","--upload","false","--dev","false","--ci","true","--refSource","datahub","--outDir","s3://bicf-nf-output/ci-env/output/Q-Y5F6_fastqoverride","--fastqsForce","s3://bicf-nf-output/ci-env/input/*.fastq.gz"]