Try redirecting out and err

.gitlab-ci.yml

@@ -105,7 +105,7 @@ integration_se:
   script:
   - hostname
   - ulimit -a
-  - nextflow run ./workflow/test.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4
+  - nextflow run ./workflow/test.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 1>> out.out 2>> err.err
 
 integration_pe:
   stage: integration