Fix test dx output location

.gitlab-ci.yml

@@ -1020,13 +1020,15 @@ dnanexus:
   except:
     variables:
       - $dnanexusEnv == "false"
+  before_script:
+    - module load dxtoolkit/python27/0.294.0
+    - 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 ${dnanexus_workspace}
   script:
     - hostname
     - ulimit -a
     - module load dxtoolkit/python27/0.294.0
     - export NXF_XPACK_LICENSE=${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/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 nf-dxapp-bicf --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} \
         --watch \
@@ -1037,3 +1039,4 @@ dnanexus:
     - module load dxtoolkit/python27/0.294.0
     - dx rm /ci-env/auth/c* --all --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace}
     - dx rm /ci-env/input/Q-Y5F6_1M.R{1,2}.fastq.gz --all --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace}
+  fail_after_scriot

docs/nxf_dnanexus-ci-test.json

 {
 	"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/input/*.fastq.gz",
+	"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"
 }