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CHANGELOG.md

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nf-core/references: Changelog

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

0.1 - Tar Tarasque

Initial pre-release of nf-core/references, created with the nf-core template. Tar is a dark grey color ( #383838), and the Tarasque is a legendary dragon from the South of France.

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
  • 43 - Add support for multiple known_indels_vcf via s3 globs
  • 47 - Add fasta assets for files in igenomes
  • 51 - Add fasta_fai assets for files in igenomes
  • 52 - Add abundantsequences_fasta, bismark_index, bowtie1_index, bowtie2_index, bwamem1_index, bwamem2_index, chrom_info, chromosomes_fasta, dragmap_hashtable, fasta_dict, genes_bed, genes_refflat, genes_refgene, genome_size_xml, gtf, hairpin_fasta, mature_fasta, readme, source, source_vcf, species, star_index and vcf assets for files in igenomes
  • 56 - Add fields for bowtie1_index, bowtie2_index, bwamem1_index, bwamem2_index, dragmap_hashtable, hisat2_index, kallisto_index, msisensorpro_list, rsem_index, salmon_index, star_index, vcf_tbi in assets
  • 56 - Add new params: kallisto_make_unique to use the --make-unique option for kallisto
  • 56 - New file assets/genomes/Caenorhabditis_elegans/NCBI/WBcel235_updated.yml, build from assets/genomes/Caenorhabditis_elegans/NCBI/WBcel235.yml
  • 62 - Added comments to the code
  • 66 - Output index

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
  • 43 - Fasta is no longer a required asset
  • 48 - Simplify VCF tabix index generation and related assets
  • 48 - Code refactoring (new subworfklows for each type of operations)
  • 49 - Better publishing for all files
  • 53 - Better publishing for all aligner indexes
  • 56 - reference_version -> source_version
  • 59 - Simplify input structure
  • 60 - Just 2 shards in CI instead of 5
  • 61 - Move assets in nf-core/references-assets
  • 62 - samplesheet -> asset
  • 62 - Refactor and simplify codebase
  • 63 - Unpack gff even when gtf is present
  • 64 - Improve documentation
  • 68 - Minor refactoring
  • 69 - Better comments

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
  • 50 - Minimal JAVA is 17
  • 51 - Fix missing fasta assets for GATK build
  • 56 - Add new logic for skip creation of existing assets
  • 62 - Remove failure when no tools are specified, because one might just want to unpack assets

Dependencies

Subworkflows

Old name New name
SAMPLESHEET_TO_CHANNEL ASSET_TO_CHANNEL
CREATE_ALIGN_INDEX_WITH_GFF CREATE_FROM_FASTA_AND_ANNOTATION
CREATE_ALIGN_INDEX CREATE_FROM_FASTA_ONLY
INDEX_FASTA CREATE_FROM_FASTA_ONLY
UNCOMPRESS_REFERENCES UNCOMPRESS_ASSET

If two subworkflows end up with the same name, it means that they have been merged into one.

Deprecated