Updated Dockers

What's Changed

• Stop drop(ing chr x) and roll by @aofarrel in #82
• Wrangle some gds files by @aofarrel in #84
• Small vcf-to-gds QOL improvements by @aofarrel in #86
• Update dockstore.yml by @aofarrel in #91
• Update ld-prune's docker and truths by @aofarrel in #94
• Update assoc-agg docker + file estimation by @aofarrel in #92

Full Changelog: v7.2.0...v7.2.1

v7.2.0 - A pile of small fixes

Several small fixes for vcf-to-gds, ld-pruning, and assoc-agg. Read the details here: #81

Full Changelog: v7.1.1...v7.2.0

v7.1.1 - The Small Checker Update

Oops, forgot to update the relevant checker workflows' links!

Full Changelog: v7.1.0...v7.1.1

v7.1.0 - The Big Data Update

Updates association aggregate, ld pruning, and vcf-to-gds to better handle large GDS file inputs. Also, association aggregate will now check at the beginning of the workflow if you put in only one file, and if you did, will exit gracefully with a hopefully-useful error. This >1 file limitation is also noted in the readme now.

Full Changelog: v7.0.1...v7.1.0

Patch edge case in assoc-agg checker 🩹

A one-line update to pull a new version of the checker workflow repo, in order to account for an odd edge case where chr2's weights files are considered non-equivalent, and then are considered equivalent, and then get a bit confused.

Implement association-aggregate

This one was difficult, but we won out in the end. Note that it has a lot of differences compared to the CWL version; see the docs for more information.

Implement PC-Relate and PC-Air

Implements PC-Air by @juklucas and PC-Relate by @aofarrel. Checker workflows included.

Hotfix vcf-to-gds on Terra

Cromwell has an issue wherein it cannot modify input files in some Docker containers on some backends, including Terra. I implemented a workaround about two months ago, but while testing a new one that would avoid having to duplicate files, I accidentally merged my testing branch to main. As the tested workaround did not work, vcf-to-gds would have no issues when run locally, but would fail on the second task when run on Terra. This release returns to the old workaround.

It should be noted this is not related to the removal of the twice-localized workaround in the last release. Those removals are still sound.

Implement KING, more efficient, DRS workaround

New Workflow

Implements KING, written by @avani-k.

Major Improvement

Workaround for Terra's basename() bug which previously caused failures on DRS inputs. The underlying problem is a Cromwell bug that cannot be fixed on my end, and this workaround will be reverted once the underlying issue is resolved.

Minor Improvement

Removes the twice-localized workaround for both LD Prune and Null Model. Previously, I thought that symlinks could not work on Terra. It turns out that vcf-to-gds is the only one with that restriction, and the restriction is ultimately due to file permissions on Terra. As vcf-to-gds was the first workflow I converted, I applied my incorrect conclusion to subsequent workflows. This has since been remedied. Although the file permissions issue has always been something I had on my list to further investigate, I'd like to thank @juklucas for championing its prioritization -- it aids not only this set of workflows, but I've also gained a better understanding of Cromwell.

Null Model + LD Prune Hotfix

Hotfix LD Prune bad workflow-level output.