2.16.10

• Fix .fastq file extension not working
• Fix .FASTQ file extension not working
• Fix VCF failsafe (only relevant in older clockwork container) not working
• Fix decontamination reports (counts out) and fastp reports not delocalizing
• Fix some double quotes which could hypothetically cause issues
• Fix 2024 mode

What's Changed

• Fix .fastq file extension and a VCF failsafe by @aofarrel in #50

Full Changelog: 2.16.9...2.16.10

2.16.9

Fixes issue with CalTBNet samples that have an underscore in their sample name. Nevertheless, those samples do not have sample names that correlate with their filenames, so for CalTBNet specifically you still have to use force_rename_out (but it works better now).

Full Changelog: 2.16.8...2.16.9

2.16.8

This would have caught a very silly issue quite a while ago.

Full Changelog: 2.16.7...2.16.8

2.16.7

UgGGGHHHHHHH

Full Changelog: 2.16.6...2.16.7

2.16.6 - Better support for 2024 mode, typo fixes

Full Changelog: 2.16.5...2.16.6

2.16.5 - Better debug outputs

Small fix to the variant caller's debug outputs so we can get the cortex and samtools VCF with regard to iqbal-lab-org/clockwork#127. Tested and passing on Terra.

2.16.4 - Failsafe for empty VCF

Full Changelog: 2.16.3...2.16.4

2.16.3

• Fix CRyPTIC Docker, which for some reason needs the minimap2 index even though the CDC-Varpipe Docker doesn't?
• Fix fallbacks for new QC metrics
• Fix a rare bug where a temporary file (seemingly created by Terra?) can be picked up as a read file because of its filename
• Make decontamination more efficient by providing a not-tarball version of the decontamination reference in the Docker image
  • untar logic is retained as a fallback in case the user selects an older version of the Docker image
• Decontamination ref is now in /ref/ instead of getting mv'd into the workdir at runtime; this wasn't tested on miniwdl but since it's an abs path this shouldn't be an issue

Full Changelog: 2.16.2...2.16.3

2.16.2

Refactor the QC stuff for combined decontamination task and stop allowing fastp filtering to happen after decontamination.

Full Changelog: 2.16.0...2.16.2

2.15.0

Go Go Go!

What's Changed

• Update dockers 0.12.5.1 (ish) by @aofarrel in #46

Full Changelog: 2.14.0...2.15.0