2.3.1 - Small runtime attrs change

Halves the default runtime attributes for the combined single decontamination.

Full Changelog: 2.3.0...2.3.1

2.3.0 - Check for duplicates

Various bugfixes and checks for duplicate samples in the combined decontamination tasks (both per sample and all-samples-at-once).

2.2.1 - Fix threads argument

Fix a typo in the threads argument of map_reads, combined_decontamination_single, and combined_decontamination_multiple

Full Changelog: 2.2.0...2.2.1

2.2.0 - Decontaminate many samples at once

You can now take in many samples worth of fastqs, via tarballs, at once when it comes to decontamination. @aofarrel in #16

Full Changelog: 2.1.0...2.2.0

2.1.0 - Combined decontamination

Adds a task that combines the map_reads call with the rm_contam call, halving the number of VMs needed.

2.0.1

Update Docker image tags. What was being called "latest" was actually v0.11.2, and that's not ideal considering v0.11.3 was released by Iqbal Lab two months ago. I've deleted the latest tag from my Docker Hub and replaced it with one tagged v0.11.2 after ensuring the digests were the same. Then, I pushed my mirror of v0.11.3 onto Docker Hub.

Tasks under active development get v0.11.3, while ones that aren't changing anytime soon stick to v0.11.2.

2.0.0

What's Changed

• TB reference files task now delocalize faster due to being pulled on an SSD instead of an HDD
• The purpose of the map_reads task has been clarified
• sample_name and outfile no longer input variables for map_reads, they are instead calculated at runtime -- and the task can handle sampleID_runID filenames
• map_reads moves the reference genome rather than copying it
• reference_prepare now works on SSDs
• remove_contam now uses the correct samtools call to avoid weird errors
• The variant calling task now has two versions (_simple and _verbose), both of which have a lot more debugging information
• Both of the new variant calling tasks now detect the most common error with variant calling -- not enough variants
• Variant calling is now done on SSDs
• General improvements for remove_contam including a move to SSDs + mv'ing instead of copying

PRs involved

• Variant call debugging files by @aofarrel in #8
• Sort by name by @aofarrel in #9
• Fix sample name by @aofarrel in #10
• Add var call debugging task by @aofarrel in #11

Full Changelog: 1.0.0...2.0.0

Initial Release

Merge pull request #7 from aofarrel/improve-var-names

Improve var names