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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Remove "running locally" md once Dockstore documentation is merged

#44 aofarrel closed 3 years ago
0
Implement king

#43 avani-k closed 3 years ago
0
Stop duplicating inputs: Documentation

#42 aofarrel closed 3 years ago
0
Stop duplicating inputs in LD Prune and Null Model

#41 aofarrel closed 3 years ago
0
Replace a paragraph with a hyperlink

#40 aofarrel closed 3 years ago
0
Add parameter_meta to all workflows

#39 aofarrel opened 3 years ago
0
Implement null model

#38 aofarrel closed 3 years ago
0
Estimate size of inputs

#37 aofarrel closed 3 years ago
0
Nullmodel rearragement

#36 aofarrel closed 3 years ago
0
[b, e] Inputs for optional files are not counted in input estimate

#35 aofarrel closed 3 years ago
4
Better readmes

#34 aofarrel closed 3 years ago
0
Update cwl-vs-wdl.md

#33 aofarrel closed 3 years ago
1
Small spacing changes, new remote file

#32 aofarrel closed 3 years ago
0
[null model] Conditional + inverse normal results in md5 mismatch

#31 aofarrel opened 3 years ago
3
R-Powered Checker Workflow

#30 aofarrel closed 3 years ago
0
Implement null model

#29 aofarrel closed 3 years ago
1
vcf-to-gds improvements

#28 aofarrel closed 3 years ago
0
Workflow level outputs

#27 aofarrel closed 3 years ago
0
[a] check_gds failure when run on full-size 1000 Genomes files

#26 aofarrel closed 3 years ago
6
Reorganize repository

#25 aofarrel closed 3 years ago
0
[e] GDS files not supported on null model report

#24 aofarrel closed 3 years ago
1
[e] null model currently does not transfer metadata to the output

#23 aofarrel closed 3 years ago
2
[b] WDL merge_GDS output and CWL merge_GDS output functionally equivalent, but do not have matching MD5sum

#22 aofarrel closed 3 years ago
4
[b] if a scattered task in the checker returns 1, the overall pipeline does not fail

#21 aofarrel closed 3 years ago
3
[b] merge_gds output fails checker in non-default case

#20 aofarrel closed 3 years ago
12
[e] unrelated phenos results in undefined columns selected error

#19 aofarrel closed 3 years ago
2
[null model] null_model_file: ghost input in the CWL

#18 aofarrel closed 2 years ago
1
[a] implement function improvements in vcf-to-gds

#17 aofarrel closed 3 years ago
1
Pull in changes to cwl-vs-wdl.md

#16 aofarrel closed 3 years ago
0
Implement merge_gds and check_merge_gds

#15 aofarrel closed 3 years ago
8
[b] exclude_PCA does not show up on SB config

#14 aofarrel closed 3 years ago
4
[b] sample_include_file and/or variant_include_file may need better test data

#13 aofarrel closed 3 years ago
1
Implement the first half of the second workflow

#12 aofarrel closed 3 years ago
1
Hotfix Terra incompatibility with subset GDS output

#11 aofarrel closed 3 years ago
1
[b] Pruned variants outfile does not include chromosome number

#10 aofarrel closed 3 years ago
1
Remove or revamp "motiviation" section of README

#9 aofarrel closed 3 years ago
0
[ld prune] ld_pruning task is hardcoded to not work on chrX

#8 aofarrel opened 3 years ago
4
Implement autoscaling of disk size

#7 aofarrel closed 3 years ago
1
Better runtime attributes

#6 aofarrel closed 3 years ago
0
Add preemptibles for first two tasks

#5 aofarrel closed 3 years ago
1
Clean up optional variables

#4 aofarrel closed 3 years ago
0
Implement dynamic sizing

#3 aofarrel closed 3 years ago
1
The Twice-Localized Workaround

#2 aofarrel opened 3 years ago
6
Cromwell memory hogging may result in sigkills + system wide Docker lockups

#1 aofarrel closed 3 years ago
5