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)