1.1.3

What's Changed

• fix: stop pushing to gpasltd by @mcolpus in #45

Full Changelog: 1.1.2...1.1.3

1.1.2

What's Changed

• fix: for asseess_genome_creation when there are no variants by @mcolpus in #44

Full Changelog: 1.1.1...1.1.2

1.1.1

What's Changed

• fix: for asseess_genome_creation when there are no indels by @mcolpus in #43

Full Changelog: 1.1.0...1.1.1

1.1.0

What's Changed

• Just updating develop with latest release by @mcolpus in #36
• feat: script to generate creation report with a mask by @mcolpus in #37
• Mmm 1561 add secret scanning to all myco pipeline repos by @bobturneruk in #38
• Mmm 1554 fix gt bug by @mcolpus in #39
• Mmm 1600/multiple contigs by @mcolpus in #40
• Rc1.1.0 by @mcolpus in #41

Full Changelog: 1.0.0...1.1.0

1.0.0

This is the version used by the ont-vs-illumina paper

What's Changed

• main into develop by @mcolpus in #28
• chore: migrate to sp3 by @ngochieu642 in #33
• chore: migrate to sp3 by @ngochieu642 in #32
• Fix/reduce ram by @mcolpus in #31
• Fix/simplify by @mcolpus in #30
• Fix/clair3 hq dp filter by @mcolpus in #29
• Rc 1.0.0 by @mcolpus in #35

Full Changelog: 0.7.0...1.0.0

0.7.0

0.7.0

• Rename final.vcf to variants.vcf, and associated channels
• Rename final.full.vcf to all_calls.vcf, and associated channels

0.6.0

0.6.0

• Mixed sites are now counted differently, to better match what Illumina counts and to be more representative.
  • Mixed sites now counts both hets (from GT=0/1 say) and having a minor population
  • Mixed indels nows counts mutations rather than sites effected. So a large het deletion is still just 1
  • Mixed clusters now uses both snps and indels

0.5.0

What's Changed

• fix: use script to run mpileup in parallel and set -d 10000 to avoid boundary errors by @mcolpus in #7
• Mmm 1101/nextflow by @mcolpus in #6
• Fix/clair3 pipeline by @mcolpus in #8
• Mmm 1160/use bcftools flags by @mcolpus in #10
• Feat/improved clair3 by @mcolpus in #9
• Simplify params by @mcolpus in #11
• ci: add CI to pull & push docker image by @ngochieu642 in #14
• Mmm 1190 mark hets by @mcolpus in #12
• Mmm 1222 clean up repo by @mcolpus in #15
• fix: remove minor alleles with strand bias by @mcolpus in #16
• feat: filter minor alleles by overall fraction of read depth by @mcolpus in #17
• fix: stop using vdb filter for bcftools by @mcolpus in #18
• fix: stop using MIN_QUAL by @mcolpus in #19
• Rc 0.5.0 by @mcolpus in #20

New Contributors

• @ngochieu642 made their first contribution in #14

Full Changelog: 0.4.2...0.5.0

0.4.2

What's Changed

• Mmm834/match sundial by @mcolpus in #5

Full Changelog: 0.4.1...0.4.2

0.4.1

What's Changed

• fix: add update to cargo lock step to bump ci by @mcolpus in #4

Full Changelog: 0.4.0...0.4.1