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CHANGELOG.md

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Change Log

All notable changes to this project will be documented in this file.

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

v3.0

This is a major update of the quicksand-build pipeline, as the structure created here can no longer be used with quicksand v1.x. Compatibility with quicksand versions v2.x is still given.

Major Changes

  • Download the NCBI taxonomy and construct the quicksand database with krakenuniq instead of kraken. Reason: The kraken-build command didnt work anymore and yielded a corrupted gzip file.
  • remove backwarts-compability with quicksand versions v1.x (taxid_map.tsv was removed from the output)
  • add --genomes flag to provide custom genomes that get integrated into the database (folder with sequences.fasta and file.map files)
  • add --taxonomy flag to provide a custom taxonomy (folder with names.dmp and nodes.dmp files). Skip download of taxonomy
  • add --gbff flag to provide a folder with the downloaded RefSeq mitochondrion file (e.g. a quicksand-build ncbi folder)

v2.0

This is a conversion of the former dsl1 code to dsl2 syntax. The major version update is only caused by the framework shift from dsl1 to dsl2. The conversion is a "quick and dirty" conversion, with a 1:1 mapping of former processes to local modules without optimization of the channels or restructuring of the code.

Major Changes

  • modularize processes to account for the dsl2 nextflow syntax

Minor Changes

  • rename --kmers to --kmer
  • accept only a single 'kmer' as input for the --kmer flag (mutiple kmers was broken)