nf-core/fastquorum: Changelog

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

[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