Ah [VS-565] output intervals and sample list #8010
Conversation
… -> GvsExtractCallset -> GvsUnified -> GvsJointVariantCalling
…users running the beta workflow
… makes a sample file list in a logical branch that may not always be taken
koncheto-broad
requested review from
rsasch,
gbggrant,
RoriCremer and
mcovarr
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Can you link to (and share the workspace for) a successful run with these new outputs? |
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8010 +/- ##
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Coverage ? 86.241%
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Sure thing! Here's the last successful run: You can also click over to the data tab and see the new columns for output_vcf_interval_files and sample_name_list. In this workspace, I made the changes necessary and directed the outputs to those spots |
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#protip if you use include a JIRA-formatted ticket id in the PR title (e.g. VS-565), JIRA will automatically link your PR from the ticket. |
koncheto-broad
changed the title
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Sorry, only thought of this after giving my 👍🏻 ; do we want to update the documentation somewhere (e.g. https://github.com/broadinstitute/gatk/blob/ah_vs_565_output_intervals_and_sample_list/scripts/variantstore/beta_docs/run-your-own-samples.md) to let users know where to find these outputs? |
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That's a good point--the documentation should be updated. I think it's safe to do so here before I updated actual workspace itself, although technically it has the potential to create a small window in which the documentation talks about features that are not there. I'll update the ticket in Jira to explicitly mention updating the documentation as well, as it should be among the AC. |
… to the "What does it return as output?" section and removed the detailed instructions containing multiple ways to dig in and locate the interval lists and the sample name lists Also, moved the note about the naming conventions of the interval lists and the vcfs up to the end of the "What does it return as output?" section as well.
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I updated the documentation for the beta document and added it to this PR as well |
koncheto-broad
deleted the
ah_vs_565_output_intervals_and_sample_list
branch
This PR does most of the work for VS-565. It exposes the interval list and the sample list to whole way up the nested WDLs to GvsJointVariantCallng.wdl
Two minor things of note:
sample_name_list is a File option and not a File because it's only computed inside of a branch of GvsExtractCallset where control_samples is false. If there is other behavior we want in the condition where it isn't computed, just let me know. This isn't an issue when it's run inside of GvsJointVariantCalling for the beta workflow though, and making it work there was the ultimate purpose of the ticket.
This PR does not fully complete the ticket. It will also require changes to the actual beta work space to add the necessary columns to the data table sample_set and change the outputs for the GvsJointVariantCalling workflow to map the new outputs to those columns. I have made these changes and test thems in my copy of the beta workflow, and can make the required changes in the one in gvs-prod once this PR is verified and merged.