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@ryanjameskennedy ryanjameskennedy released this 20 Feb 16:46
v1.0.0
da12081

[1.0.0]

Compatible with Bonsai v1.0.0.

Added

  • Light installation doc updates
  • Updated NGP config file
  • Added ska2 module process (ska_build)
  • Added ska2 to bacterial_base.nf
  • Added emmtyper module process (emmtyper)
  • Added emmtyper to Makefile
  • Added downloading of Streptococcus & Streptococcus pyogenes files to makefile
  • Added get_taxon to methods
  • Added streptococcus and streptococcus_pyogenes workflows and profiles to configs
  • Added ska filepath to yaml
  • Added optional read downsampling using seqtk
  • Added tbGradingRulesBed to IGV track
  • Added module nanoplot to check quality of raw reads from ONT
  • Added module fastq to check qc of strep samples
  • Added module hostile to remove human reads
  • Added module sccmec for typing of SCCmec cassettes in assemblies of Staphylococcus species
  • Added when operators to all modules that aren't in bacterial_base.nf
  • Added additional arguments for Resfinder when analysing Nanopore data
  • Added downloading of hostile index to Makefile
  • Added sw docs for kpneumonia, spyogenes, & streptococcus
  • Added module spatyper for typing of Spa gene in Staphylococcus aureus

Fixed

  • Interrupted installation now hard resets E.Coli. to avoid fragmented installation
  • Installation target file for streptococcus changed, to resolve interrupted installation
  • Included htslib image to natively support tabix and bgzip
  • Fixed a bug that prevented pipeline from correctly guessing misspelled profiles
  • Fixed tbprofiler related installation rules in Makefile
  • All modules can be called in one workflow -> profile determines whether they are actually executed using when statement
  • Empty channels fixed
  • Chewbbaca collection of input fixed
  • Fixed resfinder --species arg
  • Fixed nextflow.hopper.config symlinkDir
  • Removed serotypefinder from saureus workflow
  • Fixed jasen running only on the first row/sample in csv
  • Fixed channel problem by changing Channel.of([]) to Channel.value([])
  • Fixed medaka by changing --threads to -t in all the configs
  • Fixed nextflow.hopper.config re singularity image path
  • Fixed sccmec version file
  • Fixed handling of ONT samples re fastqc & postalignqc
  • Fixed io of spatyper and turned on postalignqc for ONT
  • Fixed io of resfinder for all workflows but saureus
  • Fixed input array for postalignqc

Changed

  • Removed sudo requirement from apptainer container creation (only required for older versions of apptainer) to streamline installation
  • Updated tbdb submodule
  • Moved taxon related methods to methods directory
  • Changed spyogenes genome from GCF_900475035.1 to GCF_000006785.2
  • Changed containerDir filepath for Lund configs
  • Update configs/nextflow.dev.config root fpath
  • Changed the freebayes output directory
  • Remove copy_to_cron module
  • Updated from Singularity v3.8.7 to Apptainer v1.3.6 in the CI pipeline
  • Updated PRP to version 0.11.4
  • Changed SerotypeFinder input from reads to assembly
  • Changed variable formatting of modules
  • Changed ska & sourmash filepath to symlink dir in nextflow.hopper.config & nextflow.dev.config
  • Updated Kraken db filepath in nextflow.hopper.config & nextflow.dev.config
  • Changed staphylococcus_aureus_all to saureus_all in Makefile
  • Moved all when commands to configs
  • Updated fastqc & sccmec mem settings
  • Changed model that is used in medaka_consensus to bacterial model (using --bacteria argument)
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