fastqtogenecounts - Release 1.2.1

What's Changed

• Fix incorrect directory calculation by @JoshLoecker in https://github.com/HelikarLab/FastqToGeneCounts/pull/80

Full Changelog: https://github.com/HelikarLab/FastqToGeneCounts/compare/1.2.0...1.2.1

- Python
Published by JoshLoecker about 2 years ago

fastqtogenecounts - 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 https://github.com/HelikarLab/FastqToGeneCounts/pull/78
• Fixed duplicate code blocks, use os.path.join instead of just join by @JoshLoecker in https://github.com/HelikarLab/FastqToGeneCounts/pull/79

Full Changelog: https://github.com/HelikarLab/FastqToGeneCounts/compare/1.1.0...1.2.0

- Python
Published by JoshLoecker about 2 years ago

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

New Contributors

• @JoshLoecker made their first contribution in https://github.com/HelikarLab/FastqToGeneCounts/pull/1
• @dependabot made their first contribution in https://github.com/HelikarLab/FastqToGeneCounts/pull/10

Full Changelog: https://github.com/HelikarLab/FastqToGeneCounts/compare/1.0.0...1.1.0

- Python
Published by JoshLoecker about 2 years ago

fastqtogenecounts - First Validated Release

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

- Python
Published by JoshLoecker over 4 years ago