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Handle differing workflow parameters between wts qc and wgs qc #611

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merged 3 commits into from
Aug 11, 2023
Merged

Handle differing workflow parameters between wts qc and wgs qc #611

merged 3 commits into from
Aug 11, 2023

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alexiswl
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@alexiswl alexiswl commented Aug 8, 2023 •
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WGS

        workflow_input["enable_duplicate_marking"] = True
        workflow_input["enable_rna"] = False
        # Drop rna specific parameters
        _ = workflow_input.pop("enable_rna_quantification")
        _ = workflow_input.pop("enable_rrna_filter")
        _ = workflow_input.pop("annotation_file")

WTS

        workflow_input["enable_duplicate_marking"] = False
        workflow_input["enable_rna"] = True
        workflow_input["enable_rna_quantification"] = True
        workflow_input["enable_rrna_filter"] = True

@alexiswl alexiswl added this to the Release 2.2 milestone Aug 8, 2023
@alexiswl alexiswl requested a review from victorskl August 8, 2023 11:07
@alexiswl alexiswl self-assigned this Aug 8, 2023
@victorskl victorskl added bug Something isn't working fix labels Aug 9, 2023
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Portal Release - Ocicat: Run WTS QC workflow through Portal before running Dragen WTS Tumor Only Workflow

victorskl
victorskl approved these changes Aug 9, 2023
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LGTM, Alexis!

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alexiswl commented Aug 9, 2023

Might hold this while we tinker with the rrna filtering, quant metrics etc that we might also need to add in to the wts qc configuration

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Okie, dokie..! Saw those discussion, yes.
Or, can be another PRs; all good & leave it to you..!

@victorskl victorskl mentioned this pull request Aug 9, 2023
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@victorskl victorskl linked an issue Aug 9, 2023 that may be closed by this pull request
Drop enable_duplicate_marking for WTS QC #610
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@alexiswl alexiswl mentioned this pull request Aug 10, 2023
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Related infra pull umccr/infrastructure#334

@alexiswl alexiswl changed the title Set enable duplicate marking to false for wts qc Handle differing workflow parameters between wts qc and wgs qc Aug 11, 2023
@alexiswl
Use pop, None
9ea48d1 
Dont raise error if key doesn't exist
@alexiswl alexiswl merged commit 3ab6637 into dev Aug 11, 2023
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@alexiswl alexiswl deleted the bugfix/set-enable-duplicate-marking-to-false-for-wts-qc branch August 11, 2023 02:27
victorskl added a commit to umccr/infrastructure that referenced this pull request Oct 16, 2023
@victorskl
Portal TF: Added wts_alignment_qc workflow type SSM parameter
9e903b2 
* This is mandatory for SecondaryAnalysisHelper construct. At the mo,
  both wgs_alignment_qc and wts_alignment_qc are pointing to the same
  DRAGEN workflow at ICA CWL.
* This fixes Ocicat e2e run issue at QC step in DEV.

Related
* #334
* umccr/data-portal-apis#611
@victorskl victorskl mentioned this pull request Oct 16, 2023
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Drop enable_duplicate_marking for WTS QC
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