Add earlyQC

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

Full Changelog: 4.3.1...4.4.0

4.3.1

Takes advantage of major changes to Tree Nine.

PR

• Usher revamp by @aofarrel in #28

diff

Full Changelog: 4.3.0...4.3.1

4.3.0

What's changed

• All tasks now come with a reference genome pre-packaged in their respective Docker image
  • Refprep is now skipped
  • Building trees doesn't require inputting a ref genome
• typical_tb_masked_regions is now an optional input -- if not provided, will default to a mask file located in the docker image at /mask/R00000039_repregions.bed
  • if you are generating trees, an input tree is still required (future versions will likely have a default fallback like the mask file)
• Now pulls a tagged version of fastqc instead of main
• myco_raw's timeouts now default to 0, but the other versions remain unchanged from their previous values
• Documentation improvements
• Miscellaneous improvements in prereqs

PR

• General improvements, lay groundwork for QC filtering by @aofarrel in #27

Full Changelog: 4.2.0...4.3.0

4.2.0

PRs

• Overhaul input variables, names; add new Dockers by @aofarrel in #26

Full Changelog: 4.1.3...4.2.0

4.1.3

Strain and resistance outputs now that the correct output file name, instead of "pull_report.txt". This change will prevent overwriting when transfering workflow outputs out of GCP. --> #25

Full Changelog: 4.1.2...4.1.3

4.1.2

What's Changed

• Fix multi-sample accessions by @aofarrel in #23
• Fix myco_cleaned inputs by @aofarrel in #24

Full Changelog: 4.1.1...4.1.2

4.1.1

edit: This version of myco does not handle multi-run BioSample accessions correctly and should not be used

Updates myco_sra with these new features:

• edirect should always give run accessions now (fix pulled from v1.1.9 of a SRANWRP task)
• strain and resistance information will be pulled from TBProfiler
• TBProfiler txt files will now be output, because they're prettier than the JSONs

Other versions of myco do not use the pull part of SRANWRP, nor TBProfiler, so they are unaffected.

What's Changed

• Update myco_sra to pull strain and resistance information, fix some accessions getting no output by @aofarrel in #22

Full Changelog: 4.1.0...4.1.1

4.1.0

PRs

• #20
• #21

New stuff

• Add tb profiler
• Use new refprep task's output genome for tree building

Full Changelog: 4.0.0...4.1.0

4.0.0

What's Changed

• Split myco into multiple workflows by @aofarrel in #18
• Some other stuff by @aofarrel in #19

Full Changelog: 3.1.0...4.0.0

3.1.0

• Removed the less_scattering option
• Massive overhaul to documentation
  • Some documentation is now auto-generated
  • All inputs are now documented. Every single one. Even the runtime attributes.
  • Fixes to outdated examples
• Fix fastQC calls not happening when they should (#15)
• Carry over some improvements to the variant caller (https://github.com/aofarrel/clockwork-wdl/releases/tag/2.7.0 and #15)
• Diff and report file generation can now be toggled, while still allowing the generation of bedgraphs so we don't have to store bams (https://github.com/aofarrel/parsevcf/releases/tag/1.1.4)
• Carry over adjustments and fixes to Lily's script
  • lilymaryam/parsevcf#12
  • lilymaryam/parsevcf#13
  • https://github.com/lilymaryam/parsevcf/pull/15/files
• Change some task names to avoid having unnecessary trailing underscores
• Save the user from themselves by hardcoding important defaults that should never be changed

PRs

• Remove less scattering by @aofarrel in #12
• Update autodocument-inputs with main by @aofarrel in #13
• Fix fastqc steps by @aofarrel in #15
• Develop by @aofarrel in #16
• Pin prereq, add new vcf-->diff option by @aofarrel in #17

Full Changelog: 3.0.0...3.1.0