edsu7
commented
1 year ago Fixed sanity-check to factor multiple instances of analyses. The following test now triggers properly
(base) esu@ML4909-ESU tests % nextflow run ../main.nf -profile docker,debug_qa -params-file local-test-job-2-InputFastq.json --api_token ${token}
[6d/f1f2e7] process > ArgoDataSubmissionWf:sanityCheck [100%] 1 of 1, failed: 1 ✘
[- ] process > ArgoDataSubmissionWf:checkCramReference -
[- ] process > ArgoDataSubmissionWf:pGenExp -
[- ] process > ArgoDataSubmissionWf:valSeq -
[- ] process > ArgoDataSubmissionWf:uploadWf:songSub -
[- ] process > ArgoDataSubmissionWf:uploadWf:songMan -
[- ] process > ArgoDataSubmissionWf:uploadWf:scoreUp -
[- ] process > ArgoDataSubmissionWf:uploadWf:songPub -
[- ] process > ArgoDataSubmissionWf:submissionReceipt -
[- ] process > ArgoDataSubmissionWf:printOut -
Error executing process > 'ArgoDataSubmissionWf:sanityCheck'
Caused by:
Process `ArgoDataSubmissionWf:sanityCheck` terminated with an error exit status (1)
Command executed:
main.py -x experiment-fq.v2.tsv -t 35b7ecfe-4dd8-480f-ac5a-42a9b8e6df39 -s https://submission-song.rdpc-qa.cancercollaboratory.org -c https://clinical.qa.argo.cancercollaboratory.org
Command exit status:
1
Command output:
(empty)
Command error:
Too many conflict analyses detected. Displaying subset:
Sample 'SubWf_test_01_SA_T'/'SA624380' has an existing published analysis '026e7dbd-8a7b-4ee1-ae7d-bd8a7b0ee120' for experiment_strategy 'WGS.'
Sample 'SubWf_test_01_SA_T'/'SA624380' has an existing published analysis '03d2714a-e860-48ad-9271-4ae860d8ad3d' for experiment_strategy 'WGS.'
Sample 'SubWf_test_01_SA_T'/'SA624380' has an existing published analysis '068c76dd-3806-4e0e-8c76-dd38064e0ea6' for experiment_strategy 'WGS.'
Sample 'SubWf_test_01_SA_T'/'SA624380' has an existing published analysis '07943b12-a073-4ae3-943b-12a0739ae323' for experiment_strategy 'WGS.'
Sample 'SubWf_test_01_SA_T'/'SA624380' has an existing published analysis '177e9872-a3cd-4189-be98-72a3cd01897c' for experiment_strategy 'WGS.'Adding skip flag:
(base) esu@ML4909-ESU tests % nextflow run ../main.nf -profile docker,debug_qa -params-file local-test-job-2-InputFastq.json --api_token ${token} --skip_duplicate_check
N E X T F L O W ~ version 22.04.0
Launching `../main.nf` [nostalgic_swanson] DSL2 - revision: 25b2deb5cd
WARN: Nextflow version 22.04.0 does not match workflow required version: >=22.10.0 -- Execution will continue, but things may break!
executor > local (10)
[1c/95e9b8] process > ArgoDataSubmissionWf:sanityCheck [100%] 1 of 1 ✔
[a6/cf3012] process > ArgoDataSubmissionWf:checkCramReference [100%] 1 of 1 ✔
[2f/482a27] process > ArgoDataSubmissionWf:pGenExp [100%] 1 of 1 ✔
[7b/bef740] process > ArgoDataSubmissionWf:valSeq [100%] 1 of 1 ✔
[ed/510df9] process > ArgoDataSubmissionWf:uploadWf:songSub (TEST-QA) [100%] 1 of 1 ✔
[8e/40c6d3] process > ArgoDataSubmissionWf:uploadWf:songMan (fed58b5e-ae3a-4484-958b-5eae3a5484f9) [100%] 1 of 1 ✔
[96/62eee5] process > ArgoDataSubmissionWf:uploadWf:scoreUp (fed58b5e-ae3a-4484-958b-5eae3a5484f9) [100%] 1 of 1 ✔
[a6/c03dd7] process > ArgoDataSubmissionWf:uploadWf:songPub (fed58b5e-ae3a-4484-958b-5eae3a5484f9) [100%] 1 of 1 ✔
[f7/08b539] process > ArgoDataSubmissionWf:submissionReceipt [100%] 1 of 1 ✔
[fb/3f61e8] process > ArgoDataSubmissionWf:printOut [100%] 1 of 1 ✔
Payload JSON File : /Users/esu/Desktop/GitHub/icgc-argo/argo-data-submission/argo-data-submission-wf/tests/work/2f/482a2758d1e0b339ee7226732f3825/dafe7511-4997-48d4-8013-e600e0ccbd68.sequencing_experiment.payload.json
Analysis ID : fed58b5e-ae3a-4484-958b-5eae3a5484f9
Submission TSV Receipt: /Users/esu/Desktop/GitHub/icgc-argo/argo-data-submission/argo-data-submission-wf/tests/work/f7/08b5391b0bb455e445b167ec26f41d/fed58b5e-ae3a-4484-958b-5eae3a5484f9_submission_receipt.tsv
Completed at: 09-Jan-2023 17:45:13
Duration : 1m 29s
CPU hours : 0.1
Succeeded : 10
works for both docker and singularity