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