5.1.0 - Switch to newer TBProfiler, simplify logic

What's Changed

• Better logic, use neoTBfastprofiler, add tbprofilerQC_max_pct_unmapped by @aofarrel in #37

Full Changelog: 5.0.3...5.1.0

5.0.3 - CDC decontamination + bug fixes

Changes

• Support CDC decontamination reference
• Fix some JSONs
• Fix single_sample_tbprof_bam_depth in myco_raw
• Add Terra data table for testing

PRs

• California rework (CDC decontamination reference) by @aofarrel in #38

Full Changelog: 5.0.2...5.0.3

5.0.2 - Further fix % unmapped bug

Most chances of 5.0.1 were in both myco_raw and myco_sra, but the % unmapped bugfix was not. This one-character change fixes the bug for myco_sra.

Tiny little changelog: 5.0.1...5.0.2

5.0.1 - Fix unmapped bug, better variable names

Fixed a nasty bug and changed some variable names, as described here: #36

Full Changelog: 5.0.0...5.0.1

5.0.0 - Status code reporting

As boring as tasks reporting on their status may seem, this was one of the most interesting features I've ever implemented in a WDL -- or at least, interesting to me personally. Oh, I could go on and on about the specifics of this... the deception of defined()... the use cases...

What's Changed

• Rebase main and catch-bad-samples by @aofarrel in #35
• Catch bad samples by @aofarrel in #32

Full Changelog: 4.5.2...5.0.0

4.5.2 - Filter low coverage diffs earlier

Moves the filtering out of diff files from Tree Nine into myco in order to prepare for an eventual split of myco and Tree Nine for CDPH. Also generates a (currently unused) error code output from this filtering step to be used by the in-development "put the sample filtering error in the data table" system.

PR

• Filter bad diffs before tree nine by @aofarrel in #34

Full Changelog: 4.5.1...4.5.2

4.5.1 - Looker CSVs

CSVs from this parser, which converts TBProfiler JSONs into something Looker can use, are now available as workflow-level outputs. Only the fastq version of TBProfiler ("earlyQC") is supported.

PRs

• Output CSVs for Looker and others by @aofarrel in #33

Full Changelog: 4.5.0...4.5.1

4.5.0 - Covstats filtering

You can now filter samples on the basis of information from covstats.

PR

• Implement covstats filtering by @aofarrel in #31

Full Changelog: 4.4.1...4.5.0

4.4.1 - cleanup

Yet another cleanup, plus some improvements to prereqs. Also, you can get workflow-level outputs from fastq-TBProfiler now.

PRs

• Cleanup and clarify by @aofarrel in #30

Full Changelog: 4.4.0...4.4.1

Add earlyQC

Filtering can now be done to remove fastqs with too many reads below Q30.

Full Changelog: 4.3.1...4.4.0