Release 1.2.1

What's Changed

• Fix incorrect directory calculation by @JoshLoecker in #80

Full Changelog: 1.2.0...1.2.1

Release 1.2.0

This is a fairly major release with the ability to now automatically generate or download genome-related files, such as the primary assembly, gtf, etc. files. This also comes with changes to the config.yaml file as a result

What's Changed

• Create genome reference files by @JoshLoecker in #78
• Fixed duplicate code blocks, use os.path.join instead of just join by @JoshLoecker in #79

Full Changelog: 1.1.0...1.2.0

Release 1.1.0

This is the first release in a long time simply because I didn't know if using releases was an appropriate manner of showing changes to this workflow. Because I've made this release, I've made the decision to use releases.

What's Changed

• Include usage of 'workflow.use_conda' to ensure conda is being used by @JoshLoecker in #1
• Fix Environment Installation by @JoshLoecker in #2
• Remove touch {output} by @JoshLoecker in #3
• Move FastQ_Screen_Genomes to results/ directory by @JoshLoecker in #4
• Move contaminant screen results by @JoshLoecker in #11
• Updated documentation by @JoshLoecker in #12
• Bump tzinfo from 1.2.9 to 1.2.10 in /docs by @dependabot in #10
• Move contaminant screen results by @JoshLoecker in #13
• Update CookieCutter Installation by @JoshLoecker in #17
• Install snakemake with Mamba by @JoshLoecker in #18
• Update README.md by @JoshLoecker in #19
• Update Documentation by @JoshLoecker in #22
• Remove old "Setup" from sidebar by @JoshLoecker in #23
• create results directory if not existing by @JoshLoecker in #24
• Add Conda Channels to Documentation by @JoshLoecker in #26
• Use module load mamba in Documentation by @JoshLoecker in #28
• Use module load mamba in Documentation by @JoshLoecker in #27
• Reload mamba if adding channels doesn't work by @JoshLoecker in #29
• Conda -> mamba fixes by @JoshLoecker in #30
• Lock tabulate to version 0.8.10 by @JoshLoecker in #31
• Update docs on why tabulate is locked to 0.8.10 by @JoshLoecker in #32
• Fixes to rule ordering by @JoshLoecker in #36
• Contaminant Screen missing input by @JoshLoecker in #38
• Use proper curly braces in documentation by @JoshLoecker in #39
• gunzip the GTF file by @JoshLoecker in #40
• Fix parenthesis -> braces by @JoshLoecker in #41
• Fixes for Snakemake by @JoshLoecker in #42
• Fix BED command in documentation by @JoshLoecker in #43
• Update docs on why tabulate is locked to 0.8.10 by @JoshLoecker in #44
• Update .gitignore by @JoshLoecker in #46
• Major internal changes to remove touch {output} of rules by @JoshLoecker in #50
• Bump nokogiri from 1.13.6 to 1.13.9 in /docs by @dependabot in #34
• Initial fix for contaminant screen race condition by @JoshLoecker in #53
• Bump nokogiri from 1.13.9 to 1.14.0 in /docs by @dependabot in #51
• Fix copy items if required by @JoshLoecker in #57
• Fix validation checks by @JoshLoecker in #58
• Update documentation by @JoshLoecker in #62
• Bump nokogiri from 1.14.0 to 1.14.3 in /docs by @dependabot in #59
• Bump activesupport from 6.0.4 to 6.0.6.1 in /docs by @dependabot in #54
• Fix default scratch directory by @JoshLoecker in #61
• Automatically determine delimiter in input control files by @JoshLoecker in #63
• Fix Scratch Dir Parameter by @JoshLoecker in #65
• Edit default scratch location by @JoshLoecker in #67
• Fix documentation for default profiles by @JoshLoecker in #68
• Additional fixes for documentation by @JoshLoecker in #69
• Fix default resources by @JoshLoecker in #70
• Fix configuration log file output by @JoshLoecker in #71
• Use enum values instead of hardcoded strings by @JoshLoecker in #72
• Documentation update + a lot more by @JoshLoecker in #76
• Edit default scratch location by @JoshLoecker in #66
• Bump nokogiri from 1.14.3 to 1.16.3 in /docs by @dependabot in #75

New Contributors

• @JoshLoecker made their first contribution in #1
• @dependabot made their first contribution in #10

Full Changelog: 1.0.0...1.1.0

First Validated Release

The workflow has completed a full workflow with no issues being raised.