Small updates to JointVcfFiltering WDL #8027
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| @@ -27,6 +27,8 @@ workflow JointVcfFiltering { | |||
| String indel_annotations | |||
| File? gatk_override | |||
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| Boolean use_allele_specific_annotations = false | |||
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I gave this a default, but I can also see an argument for having it be a required input since it's somewhat tied to the input annotations (which are currently required). Would love a second opinion.
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Good point. I think it makes sense to make it required.
More generally, for task-level required/optional arguments, I like the style we use in the CNV WDLs. That is, all arguments are exposed, and optional arguments have their defaults specified in the command line rather than in the parameter block (see e.g.
gatk/scripts/cnv_wdl/cnv_common_tasks.wdl
Line 34 in ef50c08
Not sure if this is the way automatic WDL generation works (haven't tried it myself), but I think it makes sense. And ideally we'd be good about using that functionality that to keep the defaults in sync between the WDL and the jar. Baby steps!
Don't worry about all that for this PR---I'll tackle it in my push. Thanks!
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Ah makes sense, it does seem cleaner to keep the defaults in the command line.
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## master #8027 +/- ##
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Coverage 86.659% 86.659%
- Complexity 38881 38885 +4
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Files 2333 2333
Lines 182340 182340
Branches 20022 20021 -1
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Hits 158014 158014
+ Misses 17300 17299 -1
- Partials 7026 7027 +1
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| @@ -27,6 +27,8 @@ workflow JointVcfFiltering { | |||
| String indel_annotations | |||
| File? gatk_override | |||
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| Boolean use_allele_specific_annotations = false | |||
There was a problem hiding this comment.
Good point. I think it makes sense to make it required.
More generally, for task-level required/optional arguments, I like the style we use in the CNV WDLs. That is, all arguments are exposed, and optional arguments have their defaults specified in the command line rather than in the parameter block (see e.g.
gatk/scripts/cnv_wdl/cnv_common_tasks.wdl
Line 34 in ef50c08
Not sure if this is the way automatic WDL generation works (haven't tried it myself), but I think it makes sense. And ideally we'd be good about using that functionality that to keep the defaults in sync between the WDL and the jar. Baby steps!
Don't worry about all that for this PR---I'll tackle it in my push. Thanks!
…input in JointVcfFiltering WDL (#8027) * Small changes to JointVCFFiltering WDL * making default for use_allele_specific_annotations * addressing comments
* Added a new suite of tools for variant filtering based on site-level annotations. (#7954) * Adds wdl that tests joint VCF filtering tools (#7932) * adding filtering wdl * renaming pipeline * addressing comments * added bash * renaming json * adding glob to extract for extra files * changing dollar signs * small comments * Added changes for specifying model backend and other tweaks to WDLs and environment. * Added classes for representing a collection of labeled variant annotations. * Added interfaces for modeling and scoring backends. * Added a new suite of tools for variant filtering based on site-level annotations. * Added integration tests. * Added test resources and expected results. * Miscellaneous changes. * Removed non-ASCII characters. * Added documentation for TrainVariantAnnotationsModel and addressed review comments. Co-authored-by: meganshand <[email protected]> * Added toggle for selecting resource-matching strategies and miscellaneous minor fixes to new annotation-based filtering tools. (#8049) * Adding use_allele_specific_annotation arg and fixing task with empty input in JointVcfFiltering WDL (#8027) * Small changes to JointVCFFiltering WDL * making default for use_allele_specific_annotations * addressing comments * first stab * wire through WDL changes * fixed typo * set model_backend input value * add gatk_override to JointVcfFiltering call * typo in indel_annotations * make model_backend optional * tabs and spaces * make all model_backends optional * use gatk 4.3.0 * no point in changing the table names as this is a POC * adding new branch to dockstore * adding in branching logic for classic VQSR vs VQSR-Lite * implementing the separate schemas for the VQSR vs VQSR-Lite branches, including Java changes necessary to produce the different tsv files * passing classic flag to indel run of CreateFilteringFiles * Update GvsCreateFilterSet.wdl cleaning up verbiage * Removed mapping error rate from estimate of denoised copy ratios output by gCNV and updated sklearn. (#7261) * cleanup up sloppy comment --------- Co-authored-by: samuelklee <[email protected]> Co-authored-by: meganshand <[email protected]> Co-authored-by: Rebecca Asch <[email protected]>
ScoreVariantAnnotations