LOGAN 0.3.3

• Fixed container mount error - removed broken paths. (#111, @samarth8392)
• Fixed input file name collision in Octopus variant calling. (#111, @samarth8392)
• Fixed AnnotSV database path resolution in tumor-only SV workflows. (#111, @samarth8392)

LOGAN 0.3.2

• Uses Nextflow v25 for logan run; fixes the bug in stub run in nf v24.10 (see: nextflow-io/nextflow#5456) (#99, @samarth8392)
• Removed old bindpaths and fixed /gs10 doesn't exist error. (#107, @samarth8392)
• Increased pipeline walltime for slurm submission to 4 days (96 hours). (#107, #108, @samarth8392)
• Minor documentation updates for setup and running LOGAN. (#107, @samarth8392)

LOGAN 0.3.1

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

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)

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