What's Changed
- Add observed resource usage by @twrightsman in #35
- decrease reference reading to one by @kubranarci in #36
- Documentation of output in output.md by @fulaibaowang in #39
- Remove duplicates by @fulaibaowang in #41
- make sure bwa_index wont fail in github actions by @kubranarci in #46
- Increase memory allocated to bwa-mem2 indexing by @twrightsman in #45
- Save workflow reports from CI by @twrightsman in #48
- clean main workflow and update reference conf by @kubranarci in #50
- change test config #51 #52 by @fulaibaowang in #53
- Read json metadata 2 by @fulaibaowang in #54
- update README.md: Add disclaimer clarifying the aim of this workflow by @Hoeze in #61
- 44 name qc value by @fulaibaowang in #63
- remvoe mosdepth restction in test config & change references to referecne for using reference by @fulaibaowang in #71
- Shared conda cache by @Hoeze in #72
- Add Slurm profile and cache conda environments in project directory by default by @Hoeze in #70
- Fix path error with submission input by @twrightsman in #77
- Convert bed file fix by @fulaibaowang in #75
- Add integration tests using tiny synthetic data + genomes by @twrightsman in #78
- Drop nf-core scaffolding by @twrightsman in #80
- Sync nf-core modules to latest and add CI lint job by @twrightsman in #81
- Remove py test by @fulaibaowang in #84
- add also collect for channels in reference path by @fulaibaowang in #89
- Migrate to GIABv3 reference for GRCh38 by @twrightsman in #88
- Sambamba by @fulaibaowang in #91
- Merge after mapping by @kubranarci in #90
- start from alignment by @kubranarci in #99
- Check for consistent formatting in Nextflow scripts by @twrightsman in #96
- Fix QC logic by @twrightsman in #100
- update-user-docs by @kubranarci in #104
- Update changelog for QC logic fixes by @twrightsman in #105
- Improve sample naming by @twrightsman in #106
- Fix paths in samplesheet.example.csv by @fulaibaowang in #107
- Samtools merge config by @fulaibaowang in #109
- Further refine default resource requirements by @fulaibaowang in #111
- Add support for long reads by @twrightsman in #103
- use conda based package instead of pip by @fulaibaowang in #117
- Rename sarek test to tiny and convert to samplesheet dataset by @fulaibaowang in #120
- Add remaining documentation for v1 by @twrightsman in #121
- Simplify reference caching by @twrightsman in #115
New Contributors
- @twrightsman made their first contribution in #35
Full Changelog: v0.2.0-alpha...v1.0.0