7.0.1 - Fix myco_raw when tbprofiler_on_bam

Fix a very silly type error masquerading as an issue with select_all(), ex:

Failed to evaluate 'coerced_bam_depths' (reason 1 of 1): Evaluating select_all(profile_bam.sample_and_median_depth) failed: For input string: "SAMEA4791117 101"

The typo doesn't exist in myco_sra and I typically run myco_raw with tbprofiler on FQs, so this has gone undetected for quite some time.

7.0.0 - Remove Tree Nine (but for good reason!!)

This project has gone through several iterations, and ultimately has two different flavors:

1. What is most practical for running on SRA data
2. What is most practical for running on health department data

Flavor 1, myco_sra, is designed to run multiple samples at once in a single instance of the workflow. When run in this way, it makes perfect sense for variant calling to feed directly into phylogenetic analysis -- all the samples are already there, so you can put everything on the tree at once.

Flavor 2, myco_raw, is also capable of running in that way, but when run on what it was actually designed to run upon (CDPH's data tables on the cloud platform Terra), we cannot combine variant calling and phylogenetics in the same workflow. Writing results back to original data tables requires each row of the data table (ie, each sample) to run its own instance of the workflow, which prevents samples from having "knowledge" of each other. Variant calling does not require "knowledge" of any other other samples, but by definition phylogenetics does.

With that in mind:

• myco is now exclusively an SRA download/FASTQ cleaner/TBProfiler/decontamination/variant-calling/QC check pipeline
• Tree Nine is, as it always was, exclusively focused on phylogenetics
• TB-D is the name for the "overall system", which will include a separate WDL file linking myco directly to Tree Nine for those who desire that functionality

For this to actually make sense, it's necessary to remove the remnants of Tree Nine from the myco pipeline -- especially as Tree Nine has changed more and more to fall into line with CDPH's specific needs.

Full Changelog: 6.4.1...7.0.0

6.4.1

myco_raw can now have date-pipelane-ran saved from previous call cached runs.

6.4.0

What's Changed

• Output ludicrous amounts of QC metrics, soften QC limits, use integers for percentages instead of floats, update decontam by @aofarrel in #53

Full Changelog: 6.3.0...6.4.0

6.3.0

Mostly a myco_raw focused release.

What's Changed

• New theiagen tbprofiler, updated clockwork, by @aofarrel in #52

Full Changelog: 6.2.5...6.3.0

6.2.5

Adds an optional low resource mode to the clockwork tasks, which allows greater concurrency on low-end non-cloud computes. Be aware that enabling this on GCP may counterintuitively result in higher costs!

6.2.4

• Fix the custom decontamination report's header not being tab-separated
• Add the counts.out TSV as a workflow-level option in myco_raw (previous release added it to myco_sra)

Full Changelog: 6.2.3...6.2.4

6.2.3

• Add citations to the top-level readme
• myco_sra now has a report task designed not to break previous call caches

Full Changelog: 6.2.2...6.2.3

6.2.2

myco_sra now detects super tiny samples in the pull task and decimated samples in the decontam task and saves you time/money/reruns by throwing out those samples quickly.

What's Changed

• Detect decimated samples by @aofarrel in #50

Full Changelog: 6.2.1...6.2.2

6.2.1

What's Changed

• Stricter guardrail by @aofarrel in #49

Full Changelog: 6.2.0...6.2.1