2.14.0

Test version for fixed cryptic decontam counts and the newest version of clockwork-wdl.

What's Changed

• Update walkthru.wdl by @aofarrel in #45
• Fix decontam counts for cryptic ref by @aofarrel in #44

Full Changelog: 2.13.0...2.14.0

2.13.0 - Detect decimated files

Combined decontamination task will now correctly detect "decimated" samples which have very few reads. This should save time and money in myco as it prevents moving onto the variant caller, and also prevents rare bugs where the variant caller freaks out due to coverage issues (most typically this manifests as having enough reads for samtools but not cortex, but it seems there's a few other possible failures too).

What's Changed

• Fix print bugs, fail tiny files in check and decontam task by @aofarrel in #36

Full Changelog: 2.12.2...2.13.0

2.12.2 - More decombo fixes

What's Changed

• Fix .gz support, better .tar support, out pct_loss by @aofarrel in #35

Full Changelog: 2.12.1...2.12.2

2.12.1 - Small combo_decontam fixes

Full Changelog: 2.12.0...2.12.1

2.12.0 - combo decontam now does fastp too!

What's Changed

• Add fastp to combined_decontam, support renaming samples by @aofarrel in #34

Full Changelog: 2.11.3...2.12.0

2.11.3 - Boost default decontamination memory

Bigger samples keep getting killed on 16 GB of memory. Although the max_retries fix in the last release does help, with the higher-coverage samples we're now working with it seems more appropriate to raise the default.

Full Changelog: 2.11.2...2.11.3

2.11.2 - Count reads, rm debug stuff in combo decontamination

What's Changed

• Count reads, rm debug stuff from combined decontamination task by @aofarrel in #33

Full Changelog: 2.11.1...2.11.2

2.11.1 - Add timers to combo decontamination

Full Changelog: 2.11.0...2.11.1

2.11.0 - CDC decontam ref, simple GitHub workflow

When running the combined decontamination task (map_reads + remove_contam), the user can now specify which Docker image they want to use. The default is the CRyPTIC 0.11.3 reference, but they can switch to the CDC reference used by varpipe instead if they wish.

Generally speaking I recommend against switching to the CDC reference if you are running on Terra -- it has a much smaller Docker image, but that's because it lacks a minimap2 index, and it appears that lack of an index file makes running the task require more memory.

Also adds a very simple miniwdl check on push to GitHub.

2.10.0 - Status Codes

Adds error/status codes to the variant caller and combined decontamination steps.

PR

• Add error/status codes to combo decontam task and main variant caller task by @aofarrel in #29

Full Changelog: 2.9.2...2.10.0