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LOGAN development version

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)

LOGAN 0.2.0

New features

  • 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

LOGAN 0.1.0

Features

  • Changed over to Nextflow CCBR template and pip packaging
    • Processes moved to modules/local directory
    • Workflows under the subworkflows/local directory
    • Processes fall under low/med/high, but added a somaticvariant caller process
    • Built AnnotSV/ClassifyCNV container (#40)
    • Converts strelka to add GT/AD column for downstream annotaiton (#55)
    • Adds hg19 genome build for for purple (#54)
    • Keeps VCF sample format as Tumor,Normal (#58)
    • Updated Docker base image to GATK 4.6, Adds cyvcf2 (for #54) Somalier 0.2.19, Muse 2.0.4 and HMFtools amber, purple, sage