nf-core/references
nf-core/references is a bioinformatics pipeline that build references, for multiple use cases
genomereferencesreproducibility
Version history
What’s Changed
- Add RNA-seq references by @edmundmiller in https://github.com/nf-core/references/pull/14
- WIP: Discussion about input parameters by @ewels in https://github.com/nf-core/references/pull/5
- Initial Sarek by @edmundmiller in https://github.com/nf-core/references/pull/17
- MERGE TEMPLATE by @maxulysse in https://github.com/nf-core/references/pull/19
- comment mags_size by @maxulysse in https://github.com/nf-core/references/pull/20
- TEMPLATE sync by @maxulysse in https://github.com/nf-core/references/pull/21
- add tests for sarek by @maxulysse in https://github.com/nf-core/references/pull/22
- Merge all script into one AND add tools selection by @maxulysse in https://github.com/nf-core/references/pull/23
- Add tests for rnaseq by @maxulysse in https://github.com/nf-core/references/pull/24
- add faidx, gffread and sizes by @maxulysse in https://github.com/nf-core/references/pull/27
- Add hisat2 by @maxulysse in https://github.com/nf-core/references/pull/28
- Add extract splice_sites by @maxulysse in https://github.com/nf-core/references/pull/29
- Hisat2 one more time by @maxulysse in https://github.com/nf-core/references/pull/30
- Add RSEM + refactor tests by @maxulysse in https://github.com/nf-core/references/pull/31
- Add kallisto, salmon by @maxulysse in https://github.com/nf-core/references/pull/32
- Handle pre-existing fai and sizes + move default test asset file by @maxulysse in https://github.com/nf-core/references/pull/33
- small refactor + adding intervals by @maxulysse in https://github.com/nf-core/references/pull/34
- Publish output by @maxulysse in https://github.com/nf-core/references/pull/35
- Fix Intervals generation by @maxulysse in https://github.com/nf-core/references/pull/36
- add tabix + small test refactor + rename bed_intervals to intervals_bed by @maxulysse in https://github.com/nf-core/references/pull/37
- fix gtf generation and dependencies by @maxulysse in https://github.com/nf-core/references/pull/39
- Trying publishing to a more complete path by @maxulysse in https://github.com/nf-core/references/pull/41
- add tests for multiple references building at once by @maxulysse in https://github.com/nf-core/references/pull/42
- Multiple again by @maxulysse in https://github.com/nf-core/references/pull/43
- Create assets for existing fasta in igenomes by @maxulysse in https://github.com/nf-core/references/pull/47
- Fix GHA - Minimal Java is 17 by @maxulysse in https://github.com/nf-core/references/pull/50
- Better publishing of all files by @maxulysse in https://github.com/nf-core/references/pull/49
- simplify TABIX generation + refactor by @maxulysse in https://github.com/nf-core/references/pull/48
- Update assets by @maxulysse in https://github.com/nf-core/references/pull/51
- Add most entried in assets by @maxulysse in https://github.com/nf-core/references/pull/52
- Better publishing for all aligner indexes by @maxulysse in https://github.com/nf-core/references/pull/53
- Final publish extended by @maxulysse in https://github.com/nf-core/references/pull/54
- Add decompress subworkflows + source_gff -> reference_version by @maxulysse in https://github.com/nf-core/references/pull/55
- Publish WBcel235 by @maxulysse in https://github.com/nf-core/references/pull/56
- Just 2 shards by @maxulysse in https://github.com/nf-core/references/pull/60
- Simplify map by @maxulysse in https://github.com/nf-core/references/pull/59
- Move assets in its own repo by @maxulysse in https://github.com/nf-core/references/pull/61
- Code-polish + refactor + add comments by @maxulysse in https://github.com/nf-core/references/pull/62
- Unpack gff even when gtf is present by @maxulysse in https://github.com/nf-core/references/pull/63
- Better docs by @maxulysse in https://github.com/nf-core/references/pull/64
- Minor code polish before soft release of v0.1 by @maxulysse in https://github.com/nf-core/references/pull/68
- Generate index out of all the generated references by @maxulysse in https://github.com/nf-core/references/pull/66
- Better comments pre-release 0.1 by @maxulysse in https://github.com/nf-core/references/pull/69
- prepare RC 0.1 by @maxulysse in https://github.com/nf-core/references/pull/70
New Contributors
- @edmundmiller made their first contribution in https://github.com/nf-core/references/pull/14
- @ewels made their first contribution in https://github.com/nf-core/references/pull/5
- @maxulysse made their first contribution in https://github.com/nf-core/references/pull/19
Full Changelog: https://github.com/nf-core/references/commits/0.1