What’s Changed

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

New Contributors

• @edmundmiller made their first contribution in #14
• @ewels made their first contribution in #5
• @maxulysse made their first contribution in #19

Full Changelog: https://github.com/nf-core/references/commits/0.1