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Published February 21, 2024 | Version 2.5.1
Software Open

nf-core/eager: [2.5.1] - Bopfingen (Patch) - 2024-02-21

  • 1. HKI Jena, MPI-EVA Leipzig
  • 2. Boehringer Ingelheim
  • 3. Max Planck Institute for Evolutionary Anthropology
  • 4. Max Planck institute for Evolutionary Anthropology
  • 5. Griffith University
  • 6. Centre for Palaeogenetics
  • 7. @seqeralabs | Stockholm
  • 8. Seqera Labs and @nextflow-io
  • 9. @imbforge
  • 10. @seqeralabs
  • 11. Humboldt University of Berlin
  • 12. Seqera Labs
  • 13. @BridgeBioAnalytics
  • 14. MPI-EVA

Description

[2.5.1] - 2024-02-21

Added

  • #1037 Added an option to deactivate the -sorted option of bedtools coverage, in case the feature file is not sorted the same way as the fasta file, albeit with the caveat this will be very slow. (♥ Thanks to @IdoBar for reporting, and contributing.)

Fixed

  • #1048 --vcf2genome_outfile parameter now gets prefixed by the sample_name and suffixed with .fasta (i.e. <sample_name>_<vcf2genome_outfile>.fasta). This ensures we avoid overwriting the output fasta of one sample with that of another when the option is provided. (♥ Thanks to @MeriamOs for reporting.)
  • #1047 Changed the row some statistics were reported in the General Stats table. The File name collision fixed in 2.5.0 (see #1017) caused these statistics to be reported in the wrong row due to an added suffix.
  • #1051 An error is now thrown if input BAM files end in .unmapped.bam, as this breaks the bam filtering process and empties the bam files in the process. (♥ Thanks to @PCQuilis for reporting.)

Dependencies

Deprecated

Files

nf-core/eager-2.5.1.zip

Files (17.9 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/eager/tree/2.5.1 (URL)