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Adopt to proviral pipeline changes #994

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merged 3 commits into from
Mar 12, 2024
Merged

Adopt to proviral pipeline changes #994

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ce82ad4
Rename "hivseqinr_results" output to "detailed_results"
Donaim Jul 25, 2023
413d062
Replace all HIVSeqinR by HIVIntact
Donaim Jul 25, 2023
977edfa
Kive: support both HIVSeqinR and HIVIntact versions of proviral
Donaim Mar 12, 2024
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5 changes: 3 additions & 2 deletions micall/monitor/kive_watcher.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,8 @@
'contigs_primers_csv',
'table_precursor_csv',
'proviral_landscape_csv',
'hivseqinr_results_tar']
'hivseqinr_results_tar', # TODO: remove when proviral is finally updated.
'detailed_results_tar']

# noinspection PyArgumentList
FolderEventType = Enum('FolderEventType', 'ADD_SAMPLE FINISH_FOLDER')
Expand Down Expand Up @@ -781,7 +782,7 @@ def run_pipeline(self,
run = self.run_proviral_pipeline(
sample_watcher,
folder_watcher,
'Proviral HIVSeqinR')
'Proviral')
return run
if pipeline_type == PipelineType.RESISTANCE:
run = self.run_resistance_pipeline(
Expand Down
4 changes: 2 additions & 2 deletions micall/tests/test_kive_watcher.py
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Expand Up @@ -1784,7 +1784,7 @@ def test_launch_proviral_run(raw_data_with_two_samples, mock_open_kive):
dataset='/datasets/112/'),
dict(argument='/containerargs/106',
dataset='/datasets/113/')],
name='Proviral HIVSeqinR on 2120A',
name='Proviral on 2120A',
batch='/batches/101',
groups_allowed=['Everyone']))

Expand Down Expand Up @@ -3007,7 +3007,7 @@ def test_collate_denovo_results(raw_data_with_two_samples, default_config, mock_

expected_cascade_path = version_folder / "denovo" / "cascade.csv"
expected_done_path = version_folder / "denovo" / "doneprocessing"
proviral_path = version_folder / "denovo" / "hivseqinr_results"
proviral_path = version_folder / "denovo" / "detailed_results"

main_scratch_path = version_folder / "scratch"
main_scratch_path.mkdir()
Expand Down
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