0.5.3

Changelog

Changes in v0.5.3

1. Added artic V4 primers
2. Organized Docker build process and output/copied script targets
3. Failsafe formatting for primers based on protocol pathing
4. Fix IGV Reference Header Bug

Previous changes in v0.5

1. fix to intermittent bug in depth threshold calculation (which sometimes caused cartoons to display many annotations for missing regions)
2. split up (and renamed) actions for staging and prerelease branches
3. updated README to include normal and development usage
4. added GPLv3+ license
5. Added support for insertions and deletions in consensus sequences.
6. Added automatic identification of pangolin ineages of consensus sequences by default.
7. Added IGV plots for all variants (as well as flagged potential variants) present in consensus sequences.
8. Moved container code from /root to /opt
9. General speed improvements.
10. 1. Programmatic length filter for step 2
    • minimum amplicon length allowed: 90% of length of shortest amplicon in scheme
    • maximum amplicon length allowed: 200nt longer than longest amplicon in scheme
11. Custom primer schemes enabled
12. nCoV-2019 primer_schemes added to repo
13. Guppy updated to v4.4.1

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

0.5.2

Changelog

Changes in v0.5.2

1. Programmatic length filter for step 2
   • minimum amplicon length allowed: 90% of length of shortest amplicon in scheme
   • maximum amplicon length allowed: 200nt longer than longest amplicon in scheme
2. Custom primer schemes enabled
3. nCoV-2019 primer_schemes added to repo
4. Guppy updated to v4.4.1

Previous changes in v0.5

1. fix to intermittent bug in depth threshold calculation (which sometimes caused cartoons to display many annotations for missing regions)
2. split up (and renamed) actions for staging and prerelease branches
3. updated README to include normal and development usage
4. added GPLv3+ license
5. Added support for insertions and deletions in consensus sequences.
6. Added automatic identification of pangolin ineages of consensus sequences by default.
7. Added IGV plots for all variants (as well as flagged potential variants) present in consensus sequences.
8. Moved container code from /root to /opt
9. General speed improvements.

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

0.5.1

Changelog

Changes in v0.5.1

1. fix to intermittent bug in depth threshold calculation (which sometimes caused cartoons to display many annotations for missing regions)
2. split up (and renamed) actions for staging and prerelease branches
3. updated README to include normal and development usage
4. added GPLv3+ license

Changes in v0.5.0

1. Added support for insertions and deletions in consensus sequences.
2. Added automatic identification of pangolin ineages of consensus sequences by default.
3. Added IGV plots for all variants (as well as flagged potential variants) present in consensus sequences.
4. Moved container code from /root to /opt
5. General speed improvements.

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

0.5.0

Changelog

Changes in v0.5.0

1. Added support for insertions and deletions in consensus sequences.
2. Added automatic identification of pangolin ineages of consensus sequences by default.
3. Added IGV plots for all variants (as well as flagged potential variants) present in consensus sequences.
4. Moved container code from /root to /opt
5. General speed improvements.

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

0.4.0

• Added IGV screenshots into report.
• Added much better support for empty files, missing barcodes, and failed intermediate steps.
• Report PDF should always be created now, even if the pipeline runs into issues.
• Configuration of two GitHub Actions for DockerHub pushes:
  • latest image built on publication of new releases
  • dev image built for pushes to master
• Some optimization to Dockerfile to decrease image size.

0.3.2

Attempting auto-creation of image tarball using GitHub Action

v0.3.1

Initial release, testing Docker build action