Argo data submission [email protected]

[edsu7]

Addressing:
#96

To test:

• with skipped tests

cd argo-data-submission/argo-data-submission-wf/tests

nextflow run ../../main.nf \
-profile docker,rdpc_qa \
-params-file local-test-job-7-InputCramJson.json \
--api_token ${API_TOKEN} \
--skip_duplicate_check true \
--ref_genome_fa ../../test_data/tiny-grch38-chr11-530001-537000.fa.gz \
--score_cpus 1 --score_mem 2 \
--skipping_tests 'c681,c683'

• without

cd argo-data-submission/argo-data-submission-wf/tests

nextflow run ../../main.nf \
-profile docker,rdpc_qa \
-params-file local-test-job-7-InputCramJson.json \
--api_token ${API_TOKEN} \
--skip_duplicate_check true \
--ref_genome_fa ../../test_data/tiny-grch38-chr11-530001-537000.fa.gz \
--score_cpus 1 --score_mem 2

Running the follow on old version 1.1.0 should result in the following

No such file: argo-data-submission-wf/tests/NO_FILE4

New version should complete without issue.

[guanqiaofeng]

Tested "with skipped tests" and "without" under [email protected] and main environment.

Got expected behaviour as described (success in [email protected]; and No such file: argo-data-submission-wf/tests/NO_FILE4 in main)

[guanqiaofeng]

looks good to me

[guanqiaofeng]

test