You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
This is a bit handwavy, but when coming in cold to a pipeline it would be nice to have some sense of:
What system resources / node type the tests assume
How long the tests are expected to run
Using pipeline-filter-RNAEditingSite as an example: the tests only require an F2, and the A-mini-N2 test takes < 1 minute while the A-full test takes >20 minutes, all of which is spent doing... something invisible to the logs?
2023-09-27 17:22:35,213 - NextFlow - INFO - executor > local (6)
2023-09-27 17:22:35,213 - NextFlow - INFO - [ea/16b92d] process > run_validate_PipeVal (1) [100%] 4 of 4 ✔
2023-09-27 17:22:35,213 - NextFlow - INFO - [61/4fd0ea] process > run_selectPositions_REDItools [100%] 1 of 1 ✔
2023-09-27 17:22:35,213 - NextFlow - INFO - [ee/4756e1] process > run_AnnotateRepeatMasker_RE... [ 0%] 0 of 1
2023-09-27 17:22:35,213 - NextFlow - INFO - [- ] process > run_AnnotateGene_REDItools -
2023-09-27 17:22:35,213 - NextFlow - INFO - [- ] process > run_FilterREDIportal_REDItools -
2023-09-27 17:22:35,213 - NextFlow - INFO -
2023-09-27 17:22:35,213 - NextFlow - INFO -
2023-09-27 17:22:35,214 - NextFlow - INFO -
2023-09-27 17:22:35,214 - NextFlow - INFO -
2023-09-27 17:22:35,214 - NextFlow - INFO - Script time --> START: 27/09/2023 17:22:25
2023-09-27 17:22:35,214 - NextFlow - INFO - Reading table...
2023-09-27 17:22:35,214 - NextFlow - INFO - Total lines: 562210
2023-09-27 17:22:35,214 - NextFlow - INFO - Filtered in lines: 266815
2023-09-27 17:22:35,214 - NextFlow - INFO - Selected lines saved on CPCG0196-F1-A-full_candidates.txt
2023-09-27 17:42:03,998 - NextFlow - INFO - Script time --> END: 27/09/2023 17:22:34
2023-09-27 17:42:03,999 - NextFlow - INFO -
2023-09-27 17:42:04,000 - NextFlow - INFO -
2023-09-27 17:42:04,032 - NextFlow - INFO - executor > local (6)
2023-09-27 17:42:04,033 - NextFlow - INFO - [ea/16b92d] process > run_validate_PipeVal (1) [100%] 4 of 4 ✔
2023-09-27 17:42:04,033 - NextFlow - INFO - [61/4fd0ea] process > run_selectPositions_REDItools [100%] 1 of 1 ✔
2023-09-27 17:42:04,033 - NextFlow - INFO - [ee/4756e1] process > run_AnnotateRepeatMasker_RE... [ 0%] 0 of 1
2023-09-27 17:42:04,033 - NextFlow - INFO - [- ] process > run_AnnotateGene_REDItools -
2023-09-27 17:42:04,033 - NextFlow - INFO - [- ] process > run_FilterREDIportal_REDItools -
Even just something like a free-form expected_duration field in the test config would be nice:
cases:
- name: A-mini-n2nf_script: ./main.nfparams_file: ./test/A-mini-n2.yamlskip: falseverbose: trueexpected_duration: 1 minute on an F2
The text was updated successfully, but these errors were encountered:
This is a bit handwavy, but when coming in cold to a pipeline it would be nice to have some sense of:
Using pipeline-filter-RNAEditingSite as an example: the tests only require an F2, and the A-mini-N2 test takes < 1 minute while the A-full test takes >20 minutes, all of which is spent doing... something invisible to the logs?
Even just something like a free-form
expected_duration
field in the test config would be nice:The text was updated successfully, but these errors were encountered: