Add dx run

.gitlab-ci.yml

@@ -1025,4 +1025,13 @@ dnanexus:
     - ulimit -a
     - module load dxtoolkit/python27/0.294.0
     - export NXF_XPACK_LICENSE=${nxf_license}
-    - 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}
\ No newline at end of file
+    - 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 $dnanexus_workspace}
+    - >
+      dx run nf-dxapp-bicf \
+        --watch \
+        --delay-workspace-destruction \
+        --instance-type mem1_ssd1_v2_x16 \
+        --input-json "$(envsubst < ./docs/nxf_dnanexus-ci-test.json)"
+    - 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

docs/nxf_dnanexus-ci-test.json

 {
-	"pipeline_url": "https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq.git -r develop",
-	"args": "-profile dnanexus --deriva dx://NextFlow_Prototype:test_data/rna-seq/auth/credential.json --bdbag dx://NextFlow_Prototype:auth/cookies.txt --repRID Q-Y5F6 --source staging --upload false --dev true --ci false --track false -with-report dx://NextFlow_Prototype:gudmap_rbk-output/Q-Y5F6_fastqoverride_report.html --refSource datahub --outDir dx://NextFlow_Prototype:gudmap_rbk-output/Q-Y5F6_fastqoverride, --fastqsForce dx://NextFlow_Prototype:test_data/rna-seq/fastq/small/*.fastq.gz",
+	"pipeline_url": "https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq.git -r env.ci",
+	"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/*.fastq.gz",
 	"license": "$NXF_XPACK_LICENSE"
 }