nf-core/references: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.0dev - [date]

Initial release of nf-core/references, created with the nf-core template.

Added

5 - Brainstorm about input
14 - nf-core/rnaseq references
17 - nf-core/sarek references
22 - Test pipeline output with nf-test for sarek
23 - Tools selection
24 - Test pipeline output with nf-test for rnaseq
27 - Add faidx, gffread, sizes generation
28 - Add hisat2 generation
29 - Add hisat2_extract_sites generation
31 - Add rsem, rsem_make_transcript_fasta generation
32 - Add kallisto, salmon generation
37 - Add tabix tbi generation
42 - Add multiple references build tests

Changed

21 - Template update for nf-core/tools v3.0.2
23 - Merge all scripts into one
31 - Test refactor: hisat2 and rsem have their own tests
33 - default.yml asset file is now in the test-dataset repo
35 - Use new output system
35 - Samtools + intervals are separate from Sarek tests now
35 - Rename bed_intervals to intervals_bed
35 - Rename rnaseq tests to tools tests
41 - Better sarek tests
41 - Better publishing for sarek related files

Fixed

19 - Use nf-core TEMPLATE
23 - No generation of bowtie2 index for sarek
30 - Deal with existing splice_sites
33 - Deal with existing faidx, sizes
36 - Deal intervals generation
39 - Fix gtf generation and dependencies

Dependencies

Deprecated