VS 483 Beta user wdl #7894
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VS 483 Beta user wdl #7894
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RoriCremer
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mcovarr
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Jun 13, 2022
mcovarr
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Jun 13, 2022
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| import "GvsUnified.wdl" as Unified | ||
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| workflow GvsVariantCalling { |
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Is the idea that this is what we will use for the beta workspace?
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Codecov Report
@@ Coverage Diff @@
## ah_var_store #7894 +/- ##
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Coverage ? 86.288%
Complexity ? 35194
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Files ? 2170
Lines ? 164888
Branches ? 17785
================================================
Hits ? 142278
Misses ? 16288
Partials ? 6322 |
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RoriCremer
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Jun 21, 2022
RoriCremer
commented
Jun 24, 2022
kcibul
reviewed
Jun 24, 2022
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| String extract_output_file_base_name = sub(callset_identifier, "\s+|\_+", "-") | ||
| String extract_table_prefix = sub(callset_identifier, "\s+|\_+", "-") | ||
| if(false) { |
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This seems unusual -- can you add a comment as to why this is necessary?
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yes! it's because I'm obnoxiously asking the user to come up with a name that I will use for the filter set name, and the prepare table names and the exported vcf / interval lists names, so I dont want any spaces
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i'll add a comment to the code too (!)
kcibul
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Jun 24, 2022
rsasch
reviewed
Jun 28, 2022
| Array[String] external_sample_names | ||
| Array[File] input_vcfs | ||
| Array[File] input_vcf_indexes | ||
| String callset_identifier |
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nit: I believe elsewhere we are using "call_set_identifier"
RoriCremer
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Jun 29, 2022
* create wrapper wdl for Beta users * update dockstore * remove dead old readme * update readme to be used by beta users * okay i thought i deleted this * update naming * update sample set creation * make wom happy * update dockstore * short term remove dir * remove samples_are_controls from unified * pr revisions * make the many optional inputs go away * dont allow illegal names * remove done tag * add public jar * remove superfluous file * dont allow spaces in filter set name either * correct the regex * rename callset id
This was referenced Mar 17, 2023
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A wrapper WDL that cuts down on excess params for our Beta users