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CHANGELOG.md

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nf-core/fastquorum: Changelog

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

[1.1.0] -- 2024-12-02

Enhancements & fixes

  • PR #98 - Update nf-core modules/subworkflows to most recent versions

  • PR #93 - Allow non-gzipped input fastq files

  • PR #90 - Update dependency versions in fastquorum environments

    Dependency Previous Version New Version
    bwa 0.7.17 0.7.18
    fgbio 2.0.2 2.4.0
    samtools 1.16.1 1.21
    Module Previous SHA New SHA
    bwa/index e0ff65e 6666521
    fastqc b49b899 6666521
    fgbio/sortbam 2fc7438 bc6d86f
    multiqc fe9614c cf17ca4
    samtools/dict 3c8fd07 b13f07b
    samtools/faidx 04fbbc7 b13f07b
    samtools/merge 04fbbc7 b13f07b

  • PR #87 - Raise minimum Nextflow version to 24.04.2

  • PR #84 - Update to nf-core/tools template version 3.0.2

  • PR #79 and PR #80 - Publish aligned consensus bai file

Credits

Special thanks to the following for their contributions to the release:

[1.0.1] -- 2024-09-10

Credits

Special thanks to the following for their contributions to the release:

Enhancements & fixes

  • PR #51 - Fixes a bug where alignment and filtering where swapped in the phase 2 high-throughput diagrams (@jfy133).
  • PR #58 - Prepare genome steps now run only if the corresponding parameters are not passed.
  • PR #60 - Enable automatic escalation of memory for FilterConsensusReads.
  • PR #67 - Fix setting the parameters from igenomes.
  • PR #68 - Temporary fix to merging BAMs across lanes in template-coordinate order. Using fgbio SortBam after samtools merge. Related to samtools#2062.
  • PR #71 - Add stubs to all local modules.

[1.0.0] -- 2024-05-20

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

Credits

Special thanks to the following for their contributions to the release:

Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

Enhancements & fixes

  • PR #44 - Updated bwa index to version 0.7.18
  • PR #38 - Add support for samples to have multiple runs or lanes
  • PR #38 - Improved sample sheet validation
  • PR #38 - Support one to four FASTQs per sample (e.g. when the UMI is in the index read)
  • PR #38 - Report the versions for all tools
  • PR #36 - Added significant documentation, along with publishDir module config
  • PR #33 - Add high-throughout mode (via --mode ht), with R&D mode via --mode rd being the default.
  • PR #30 - Update to nf-core template v2.14.1
  • PR #30 - Add tests using nf-core/test-datasets PR #1200
  • PR #30 - Params enable_conda was removed
  • PR #14 - Add mulled container for docker/singularity
  • PR #32 - Remove duplicate line in README
  • PR #18 - Fix pipeline when strategy is not 'Paired'
  • PR #7 - Add missing samtools conda requirement
  • PR #8 - Make it work locally