Added flag for indel realignment (-indelrealign). Potentially helpful for some variant callers that do not perform local realignment
All downstream bams will use the indel realigned files.
Issues
Adds #38
PR Checklist
(~Strikethrough~ any points that are not applicable.)
[x] This comment contains a description of changes with justifications, with any relevant issues linked.
~- ~[ ] Write unit tests for any new features, bug fixes, or other code changes.~ testing framework not yet implemented~
~- [ ] Update docs if there are any API changes.~
[x] If a new nextflow process is implemented, define the process container and stub.
[x] Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/
Changes
Added flag for indel realignment (
-indelrealign). Potentially helpful for some variant callers that do not perform local realignment All downstream bams will use the indel realigned files.Issues
Adds #38
PR Checklist
(~Strikethrough~ any points that are not applicable.)
containerandstub.CHANGELOG.mdwith a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/