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Recent Releases of logan

logan - LOGAN 0.3.1

  • Improve help message for logan run. (#97, @kelly-sovacool)
    • the default --mode is now slurm.

- Nextflow
Published by github-actions[bot] about 1 year ago

logan - LOGAN 0.3.0

  • LOGAN now depends on ccbr_tools v0.4 for updated jobby & spooker utilities. (#95, @kelly-sovacool)
  • Fix fastq naming in fastp. (#73, @dnousome)
  • Fix resources for qualimap bamqc. (#79, @dnousome)
  • Now using the readthedocs theme for the docs website. (#84, @kelly-sovacool)
  • LOGAN is now archived in Zenodo with DOI 10.5281/zenodo.14907169. (#87, @kelly-sovacool)
  • CLI updates: (#93, @kelly-sovacool)
    • Use nextflow run -resume by default, or turn it off with logan run --forceall.
    • Add --output argument for logan init and logan run.
    • If not provided, commands are run in the current working directory.
    • This is equivalent to the nextflow $launchDir constant.
    • The nextflow preview is printed before launching the actual run.
    • Set the publish_dir_mode nextflow option to link by default.
    • Set the process.cache nextflow option to deep by default rather than lenient on biowulf.
  • Sequenza chromosome M was removed for CNV analysis and all chromosomes used by default (#91, @dnousome)
  • Increased memory and lscratch allocation for applybqsr process (#91, @dnousome)
  • Manta output order was listed incorrectly (#91, @dnousome)
  • Additional hg19 genome references were fixed (#91, @dnousome)
  • Vardict Tumor only mode filtering using INFO/DP vs DP only (#91, @dnousome)
  • Fix for Deepvariant to allow sample name filtering (#91, @dnousome)

- Nextflow
Published by github-actions[bot] about 1 year ago

logan - v0.2.0

  • Added additional SV callers(GRIDSS) and annotation for SV (GRIPSS) + CNV Callers (ASCAT, CNVKit) + SNV (#66Deepsomatic)
  • Adds ffpe filtering #67
  • Bugfixes for hg19 by fixing references
  • Updated PON for hg38 using TCGA/GDC references #59
  • In development: adding exome support by using bed file to restrict calling regions
  • Refactored modules to be similar to nf-core
  • Fix error in varscan #71
  • Created separate docker #63

- Nextflow
Published by dnousome over 1 year ago