Recent Releases of aquascope
aquascope - v3.2.0
What's Changed
- Remove code related to nf-core Validation and update to nf-core Schema completed by @slsevilla in https://github.com/CDCgov/aquascope/pull/83
- update config to handle RHEL8 environment
Full Changelog: https://github.com/CDCgov/aquascope/compare/v3.1.0...v3.2.0
- Nextflow
Published by slsevilla over 1 year ago
aquascope - v3.1.0
What's Changed
- updated the usage documents @SuchiC23 #75
- Added iontorrent sample sheet information @SuchiC23 #74
- Updated the Multiqc to version 1.25.1 @SuchiC23 #72
- fix typo in samplesheet @slsevilla in #78
- add iontorrent test to CI/CD @slsevilla in #78
- reformat, add platform names to docs @slsevilla in #78
New Contributors
- @SuchiC23 made their first contribution in https://github.com/CDCgov/aquascope/pull/74
Full Changelog: https://github.com/CDCgov/aquascope/compare/v3.0.0...v3.1.0
- Nextflow
Published by slsevilla over 1 year ago
aquascope - v3.0.0
What's Changed
- Feature docs by @arunbodd in https://github.com/CDCgov/aquascope/pull/56
- NF-core template update, added three new entry points by @slsevilla in https://github.com/CDCgov/aquascope/pull/60
- Added CI workflow to test the pipeline by @antongray1 in https://github.com/CDCgov/aquascope/pull/62
- Updated readme to trigger mkdocs workflow by @antongray1 in https://github.com/CDCgov/aquascope/pull/65
- Removed redundant code by @slsevilla in f879ac397a3b13fd6136e01fa04f9ed119b3094f
- Updated FREYJA version by @slsevilla in 7d615c8b9bf33272025d0ded0770ed7650db287a (fixes #58)
- Removed IVAR Variant calling in c01698754e10d63af4b700f4feacfb1ed701fcbb (fixes #61 )
- Removed Samtools FAIDX by @slsevilla in c8163ad7c419570da881153ca90dd5d435a6ac03 (fixes #71 )
- Update schema requirements by @slsevilla in f98393af109e5ff9592dff27b449eaf982f899b1
- Fix samplesheet col name inconsistency by @slsevilla in 2a511d6b013aa67262363669169d33e3c5abd5d1 (issue #66 )
- Fixes docker issue by adding quay.io by @slsevilla in e0066f1bf608761b8434e7d72133fe652efb2cee (issue #68)
New Contributors
- @antongray1 made their first contribution in https://github.com/CDCgov/aquascope/pull/62
Full Changelog: https://github.com/CDCgov/aquascope/compare/v2.3.1...v3.0.0
- Nextflow
Published by slsevilla over 1 year ago
aquascope - v2.3.0
What's Changed
- chore: remove conflicting code by @arunbodd in https://github.com/CDCgov/aquascope/pull/51
- Add test profile for ONT data, add test data, update configs, cleanup gitignore files by @slsevilla in https://github.com/CDCgov/aquascope/pull/49
- Rebase dev from testprofiles, add new config by @arunbodd in https://github.com/CDCgov/aquascope/pull/50
- Rebasing dev to main after issues with previous merge by @slsevilla in https://github.com/CDCgov/aquascope/pull/52
Full Changelog: https://github.com/CDCgov/aquascope/compare/v2.2.1...v2.3.0
- Nextflow
Published by SuchiC23 almost 2 years ago
aquascope - v2.2.0
What's Changed
- Re: Reheader Bam issue addressed by @arunbodd in https://github.com/CDCgov/aquascope/pull/40
- Merge pull request #40 from CDCgov/dev by @arunbodd in https://github.com/CDCgov/aquascope/pull/47
- Update images, samplesheet updates, rehead BAM by @slsevilla in https://github.com/CDCgov/aquascope/pull/45
Full Changelog: https://github.com/CDCgov/aquascope/compare/v2.1.0...v2.2.0
- Nextflow
Published by slsevilla about 2 years ago
aquascope - v2.1.0
What's Changed
- Updated README and user-docs by @slsevilla @arunbodd in #29, #30, #33
- Feature Add: Amino Acid calling, threshold features added #27 by @arunbodd @schavan023 in https://github.com/CDCgov/aquascope/pull/31
Full Changelog: https://github.com/CDCgov/aquascope/compare/v2.0.0...v2.1.0
- Nextflow
Published by slsevilla about 2 years ago
aquascope - v2.0.0
What's Changed
- Update README.md by @SMorrison42 in https://github.com/CDCgov/aquascope/pull/12
- Hseabolt patch 1 by @slsevilla in https://github.com/CDCgov/aquascope/pull/25
- Docs Overhaul, CI addition, IVAR feat add by @slsevilla in https://github.com/CDCgov/aquascope/pull/21
- feat: Added processing of Ion-torrent Bams and ONT long reads
- feat: Added Nanoplot as Quality metrics tool for ONT long reads
- feat: Samtools ampliconclip is used as primary trimming tool for ONT-long reads.
- fix: removed ivar trim which was erroring for ONT-long reads
- refactor: specify primer bed file as 7th column in samplesheet - refer to ReadME file
- refactor: Qualimap Bamqc and Ivar variant calling now use "gff" file as one of the parameters, instead of bed or gff3 file formats.
- fix: Removed parameter --fai (fasta index), it now builds using samtools faidx
- feat: MultiQC report shows Freyja Demix results.
- feat: fasta and gff are now defaulted to assets folder. User input required to change these references (We strongly suggest users * * not to use a different reference, as it may lead to accession ID conflicts downstream)
- docs: updated README
- docs: update CHANGELOG format
- docs: created a VERSION log
- ci: added github actions for deployment
New Contributors
- @SMorrison42 made their first contribution in https://github.com/CDCgov/aquascope/pull/12
- @slsevilla made their first contribution in https://github.com/CDCgov/aquascope/pull/25
Full Changelog: https://github.com/CDCgov/aquascope/compare/1.0.0...v2.0.0
- Nextflow
Published by slsevilla about 2 years ago