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

6.2.0

What's Changed

• Overhaul of myco_sra by @aofarrel in #48
• Update prereqs of myco_raw by @aofarrel in #47

Full Changelog: 6.0.1...6.2.0

6.1.0 - New VCF->Diff script for VCF filtering

Full Changelog: 6.0.1...6.1.0

6.0.1 - Fix .gz fastqs

• Fixes .gz fastqs not being found in the combine, check, and decontam task
• You can now enter .tar files of multiple fastqs as an input, and it will be handled correctly (developed to be used downstream of sranwrp's download-by-bioproject)
• Attempts to calculate percentage of reads lost to contamination and fastp cleaning (task-level output only)

What's Changed

• Fix gz inputs, better support tar inputs by @aofarrel in #46

Full Changelog: 6.0.0...6.0.1

6.0.0 Revamp myco_cleaned into myco_simple

What's Changed

• Update and revamp "myco_cleaned" (myco_simple) by @aofarrel in #40

Full Changelog: 5.5.0...6.0.0

5.5.0 - Major Refactor

What's Changed

• Refactor some of the underlying WDL
• fastp now runs before decontamination instead of after by default, but this can be adjusted
• Input variables mostly make sense now, and there are fewer than before
• Implemented common-sense guardrails to prevent rogue samples jacking up cloud costs
• Fix oversized Docker images being, well, oversized
• Update and fix some outdated documentation

PR with more information

--> Refactor & run fastp before decontam & guardrail mode by @aofarrel in #45

Full Changelog: 5.4.0...5.5.0

5.4.0 - Checker workflow for myco_raw

This provides a good framework for comparing outputs after making changes to QC tolerances and/or refactoring. More or different samples will eventually be added to ensure proper edge cases are covered. Truth files may change over time.

Note that some of the Terra data tables in this version include URIs to a Terra workspace. Those URIs will only work for me. They'll be changed once I have more "final" truth files post refactor.

PR

• Add checker workflow for myco_raw by @aofarrel in #44

Full Changelog: 5.3.2...5.4.0