Env.ci

Make environment tests for DNAnexus and AWS

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated
• Replace dag.png with the most recent CI pipeline integrated_pe artifact
• [ ] Replace software_versions_mqc.yaml with the most recent CI pipeline generateVersions artifact
• [ ] Replace software_references_mqc.yaml with the most recent CI pipeline generateVersions artifact
• CHANGELOG.md is updated
• README.md is updated
• [ ] LICENSE.md is updated with new contributors
• [ ] Docker images moved to production release and changed in pipeline
• [ ] Docker images used in the CI unit tests match those used in pipeline

• ~~[ ] Close issue~~ Closes #

/cc @ghenry @venkat.malladi

.gitlab-ci.yml

@@ -1025,15 +1025,15 @@ dnanexus:
     - ulimit -a
     - module load dxtoolkit/python27/0.294.0
     - export NXF_XPACK_LICENSE=${nxf_license}
-    - dx upload ./test_data/auth/c* --path ${dnanexus_workspace}:/ci-env/auth/ --parents --auth-token ${dnanexus_authToken} --workspace-id ${dnanexus_workspace}
-    - dx upload ./test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz --path ${dnanexus_workspace}:/ci-env/input/ --parents --auth-token ${dnanexus_authToken} --workspace-id ${dnanexus_workspace}
+    - 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/small/Q-Y5F6_1M.R{1,2}.fastq.gz --path /ci-env/input/ --parents --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace}
     - >
-      dx run --auth-token ${dnanexus_authToken} --workspace-id ${dnanexus_workspace} --project ${dnanexus_workspace} nf-dxapp-bicf \
+      dx run --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} nf-dxapp-bicf \
         --watch \
         --delay-workspace-destruction \
         --instance-type mem1_ssd1_v2_x16 \
         --input-json "$(envsubst < ./docs/nxf_dnanexus-ci-test.json)"
   after_script:
     - module load dxtoolkit/python27/0.294.0
-    - dx rm ${dnanexus_workspace}:/ci-env/auth/c* --all
-    - dx rm ${dnanexus_workspace}:/ci-env/input/Q-Y5F6_1M.R{1,2}.fastq.gz --all
+    - dx rm /ci-env/auth/c* --all --project-context-id ${dnanexus_workspace}
+    - dx rm /ci-env/input/Q-Y5F6_1M.R{1,2}.fastq.gz --all --project-context-id ${dnanexus_workspace}