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CHANGELOG.md

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Changelog

unreleased

[v1.1.0] - 2024-11-08

Added

  • bwa mem as short-read mapper alternative, parameter: --bwa

[v1.0.3] - 2024-08-08

Added

  • Set default branch to main instead of the Nextflow default master
  • Remove conda clean from GitHub action to avoid random crashes
  • Bump github action versions for node 16 -> 20 change
  • Add T2T homo sapiens genome as additional auto-download option

[v1.0.2] - 2024-05-17

Added

  • added --skip_qc option to skip QC steps

[v1.0.1] - 2024-03-15

Added

  • SARS-CoV-2 added to the auto-download option

[v1.0.0] - 2024-01-04

Changed

  • reorganized of results directory and file names

Added

  • dry run CI tests
  • options to reduce disk usage
    • --cleanup_work_dir and --no_intermediate

Fixed

  • fixed some issues on Mac OS

[v1.0.0-beta.1] - 2023-10-11

Changed

  • changed minimap2 container so that ncurses is included

[v1.0.0-beta] - 2023-09-30

Changed

  • changed input parameter usage:
    • before: --[nano|illumina|illumina_single_end|fasta]
    • now: --input_type [nano|illumina|illumina_single_end|fasta] --input *.fastq
  • changed workflow figure to a nicer figure
  • changed workflow structure (introducing subworkflows)
  • input files with the suffix clean are not allowed

Added

  • added CHANGELOG.md, Citations.md and citation information
  • added --cleanup_work_dir to remove work dir files after a successful run
  • added --min_clip to filter mapped reads by soft-clipped length
  • added --dcs_strict to use only DCS reads with artificial ends
  • added stub command for Nextflow prototyping
  • added idxstats

Fixed

  • pipeline report with timestamp
  • --split-prefix parameter for minimap2
  • make concat contamination more efficient