From f9e50ab2ce01c458f374571bfdc2f1629a07faa8 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 12 Apr 2021 22:21:19 -0500
Subject: [PATCH] Update aws resources
---
.gitlab-ci.yml | 12 ++++++------
docs/nxf_aws-ci-test.json | 2 +-
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 777081d..14426c6 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 580c845..f802db6 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"]
--
GitLab