Finalize pre release

.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\

CHANGELOG.md

-# 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)

docs/nxf_aws-ci-test.json

-["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"]

docs/nxf_dnanexus-ci-test.json

 {
-	"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}"
 }