DataBiosphere analysis_pipeline_WDL issues

DataBiosphere / analysis_pipeline_WDL

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.

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Update ld-prune's docker and truths

#94 aofarrel closed 2 years ago
0
[assoc-agg] Update Docker image

#93 aofarrel closed 2 years ago
0
Update assoc-agg docker + file estimation

#92 aofarrel closed 2 years ago
2
Update dockstore.yml

#91 aofarrel closed 2 years ago
0
Create assoc-aggregate-one-gds.wdl

#90 akmanning opened 2 years ago
0
[ld prune] Update Docker image

#89 aofarrel closed 2 years ago
4
[vcf2gds] Update Docker image

#88 aofarrel closed 2 years ago
0
Reorganize test/truth data

#87 aofarrel opened 2 years ago
1
Small vcf-to-gds QOL improvements

#86 aofarrel closed 2 years ago
2
[assoc-agg] Further improve disk size estimation for prepare segments task

#85 aofarrel opened 2 years ago
0
Wrangle some gds files

#84 aofarrel closed 2 years ago
0
[assoc-agg] Does CWL still have weirdness with chrX? what is that weirdness anyway?

#83 aofarrel opened 2 years ago
0
Stop drop(ing chr x) and roll

#82 aofarrel closed 2 years ago
3
Miscellaneous fixes

#81 aofarrel closed 2 years ago
4
[assoc-agg] Bash syntax error if genome_build (and likely others) not specified in wdl_validate_inputs task

#80 aofarrel closed 2 years ago
0
Update docker

#79 aofarrel closed 2 years ago
2
[assoc-agg] RScript error in does not trigger pipeline error

#78 aofarrel closed 2 years ago
1
[assoc-agg] Implement dot product scatter

#77 aofarrel opened 2 years ago
0
Run all checker workflows from a single script

#76 aofarrel opened 2 years ago
0
Beef up default runtime args

#75 aofarrel opened 2 years ago
1
Hotfix assoc agg

#74 aofarrel closed 2 years ago
1
Make it clearer what workflows need to be run on >1 file

#73 aofarrel closed 2 years ago
1
Revamp readmes

#72 aofarrel closed 2 years ago
0
[ld-prune] If only 1 file input, error will incorrectly claim you've duplicate sample/variant IDs

#71 aofarrel closed 2 years ago
1
[assoc-agg] weight_chr2.RData is both equivalent and not equivalent to its checker file

#70 aofarrel opened 2 years ago
0
Assoc-agg checker hotfix

#69 aofarrel closed 2 years ago
0
Association aggregate

#68 aofarrel closed 2 years ago
0
[assoc-agg] If not including all chrs in assoc-agg, you must use a numerically continuous group of chrs (excluding sex chrs)

#67 aofarrel closed 2 years ago
1
[assoc-agg] Prepare segments drops chrX

#66 aofarrel closed 2 years ago
1
assoc prepare segments task errors out on non-autosomes

#65 aofarrel closed 2 years ago
1
1KG_phase3_subset_chrX.gds not equal in its two locations

#64 aofarrel opened 2 years ago
0
Weirdness in position output

#63 aofarrel closed 2 years ago
3
[assoc-agg] Are chromosomes put in numeric order in CWL plot task?

#62 aofarrel opened 2 years ago
0
#58 fails in plot step

#61 aofarrel closed 2 years ago
8
Association aggregate is not grouping correctly.

#60 aofarrel closed 2 years ago
1
Mismatch in some, not all, assoc-agg outputs

#59 aofarrel closed 2 years ago
3
Assoc Aggregate: Now With Good Scattering!

#58 aofarrel closed 2 years ago
2
Association Aggregate

#57 aofarrel closed 2 years ago
1
Pc air -- after incorporating Ash's suggestions

#56 juklucas closed 3 years ago
0
Pc air

#55 juklucas closed 3 years ago
0
First 60% of assoc-aggregate

#54 aofarrel closed 3 years ago
1
Implement PC-Relate

#53 aofarrel closed 3 years ago
1
Implement king

#52 avani-k closed 3 years ago
1
[king] md5 mismatch for 2/3 outputs

#51 avani-k opened 3 years ago
1
Update king doc

#50 avani-k closed 3 years ago
1
PCrelate checker: Mismatch in output filenames

#49 aofarrel closed 3 years ago
1
Is kinship_method hardcoded on the CWL?

#48 aofarrel closed 3 years ago
2
Hotfix drs URIs in vcf-to-gds

#47 aofarrel closed 3 years ago
2
vcf-to-gds fails on controlled access data

#46 aofarrel closed 3 years ago
1
Implement king

#45 avani-k closed 3 years ago
0