Collection of WDL workflows based off the University of Washington TOPMed DCC Best Practices for GWAS. The WDL structure was based upon CWLs written by the Seven Bridges development team.
The google bucket should have the same format as the GitHub copy, whenever possible, to better ensure congruency.
Possible way to do this:
[ ] github.com|uw-gac|analysis_pipeline|testdata or github.com\uw-gac\analysis_pipeline\testdata (backslashes would be better if JSONs can support that)
[x] vcf2gds
[x] ld_prune
[ ] assoc_agg
[ ] pc_air
[ ] pc_relate
[ ] king
each workflow should get ins/ and outs/ plus a copy of the raw CWL and an info.txt
might also be worth having archives of old truth files
Finish this reorg after fixing ld-prune, but before any other docker changes. Alisa Manning will need corrected JSONs to run testing on her new pipeline.
The google bucket should have the same format as the GitHub copy, whenever possible, to better ensure congruency.
Possible way to do this:
each workflow should get ins/ and outs/ plus a copy of the raw CWL and an info.txt
might also be worth having archives of old truth files