From 50b56cab4efdafe58e8bdc43055522cb99051956 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 20 Mar 2021 21:26:35 -0500
Subject: [PATCH] Finalize pre release
---
.gitlab-ci.yml | 2 ++
CHANGELOG.md | 2 +-
docs/nxf_aws-ci-test.json | 2 +-
docs/nxf_dnanexus-ci-test.json | 4 ++--
4 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 87348e6..da81bec 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=$(aws batch submit-job\
--job-name nf-GUDMAP_RBK_ci-env\
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 36020f0..f111685 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,4 @@
-# v2.0.0rc02
+# v2.0.0
**User Facing**
* Endness metadata "Single Read" changed to "Single End" in data-hub, pipeline updated to handle (#110) ("Single Read" still acceptable for backwards compatibility)
* Strandedness metadata "yes"/"no" changed to boolean "t"/"f" in data-hub, pipeline updated to handle (#70) ("yes"/"no" still acceptable for backwards compatibility)
diff --git a/docs/nxf_aws-ci-test.json b/docs/nxf_aws-ci-test.json
index de8752b..1de3108 100644
--- a/docs/nxf_aws-ci-test.json
+++ b/docs/nxf_aws-ci-test.json
@@ -1 +1 @@
-["utsw-bicf/gudmap_rbk.rna-seq","-r","env.ci","-profile","aws","--deriva","s3://bicf-output/ci-env/auth/credential.json","--bdbag","s3://bicf-output/ci-env/auth/cookies.txt","--repRID","Q-Y5F6","--source","staging","--upload","false","--dev","false","--ci","true","--track","false","-with-report","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride_report.html","--refSource","datahub","--outDir","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride","--fastqsForce","s3://bicf-output/ci-env/input/*.fastq.gz"]
+["utsw-bicf/gudmap_rbk.rna-seq","-r","${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 cb523c7..e4dde61 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}"
}
--
GitLab