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nf-core/pairgenomealign v2.2.0 – Chagara ponzu

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@charles-plessy charles-plessy released this 10 Jul 12:58
· 79 commits to master since this release
2.2.0
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v2.2.0 "Chagara ponzu" - [May 29th 2025]

Added

  • Support for export to BAM and CRAM formats (#31) (#43).
  • SAM/BAM/CRAM alignments files are sorted and their header features all sequences of the target genome.
  • Report ungapped percent identity (#46).
  • Update full-size test genomes to feature more T2T assemblies (#59).
  • Use a single mulled container for LAST, Samtools and open-fonts, to save ~280 Mb of downloads (#58).
  • Allow export to multiple formats (comma-separated list) (#42).
  • Allow skipping of the assembly QC with --skip_assembly_qc (#53).

Dependencies

Dependency Old version New version
SAMTOOLS_BGZIP 1.21
SAMTOOLS_DICT 1.21
SAMTOOLS_FAIDX 1.21

Parameters

Old parameter New parameter
--skip_assembly_qc

Fixed

  • Remove noisy tag in the MULTIQC_ASSEMBLYSCAN_PLOT_DATA local module (#64).
  • Restore BED format support (#56).
  • Document the multiqc_train.txt and multiqc_last_o2o.txt aggregating alignment statistics (#52).
  • Point the test configs samplesheets to nf-core/test-datasets in order to run the AWS full tests (#62).
  • Update metro map, in white background (#71).
  • Removed the last/mafswap module, which was actually not used.
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