8000 Release v1.1.0 · genomic-medicine-sweden/jasen · GitHub
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@ryanjameskennedy ryanjameskennedy released this 13 Jun 09:26
v1.1.0
2b42f67

[1.1.0]

Added

  • Added missing tools to S. aureus subworkflow tool list
  • Added spyogenes bed file representing cgmlst targets
  • Added prodigal image download to container Makefile
  • Added module for mapping long reads with Minimap2
  • Added Minimap2 refence index referenceGenomeMmi for all species
  • Added samtools_coverage to get stats from mapping long reads to the reference and assembly
  • Added minimap2_align_assembly
  • Added minimap2_index for assembly indexing
  • Added when operator to samtools for nanopore
  • Added assay to yaml output
  • Added staphylococcus_nrl profile
  • Added release_life_cycle via profiles
  • Added create_prp_yaml.py to bin
  • Added spatyper and sccmec to yaml
  • Added gambitcore as a module
  • Added apptainer and singularity profiles

Fixed

  • Fixed stub-run for S.aureus ONT workflow
  • Fixed typing error in Makefile
  • Fixed checking out pipeline code with submodules
  • Fixed genome downloading via bin/download_ncbi.py with timed retries
  • Fixed dirty submodules in .gitmodules
  • Fixed dubious ownership bug where finder dbs retrieve commit ID

Changed

  • Changed spyogenes genome from GCF_000006785.2 to GCF_005164585.1
  • Updated check_taxon method to include spyogenes
  • Changed ptf downloading to generation of ptf via prodigal for ecoli & spyogenes
  • Renamed index created by BWA from referenceGenomeIdx to referenceGenomeFai
  • Renamed bwa_mem_dedup to bwa_mem_assembly
  • Split samtools_sort into two modules
  • Removed abritamr as it's not used
  • Changed dirname container to containers
  • Changed dirname configs to conf
  • Changed dirname nextflow-modules to modules
  • Changed importing of spades
  • Updated Makefile re dir name changes
  • Updated subworkflows
  • Grouped most workflows into one (bacterial_general.nf) to remove duplicate code
  • Changed to have only one main config nexflow.config
  • Changed cmd module name to cdm
  • Updated bonsai-prp to v1.3.1
  • Changed indentation structure
  • Moved platform to config via params.platform
  • Changed hostile io
  • Updated docs regarding restructuring
  • Changed prp sub commands
  • Updated CI GA workflow re container_dir
  • Removed check-and-reinit-git-submodules from CI GA workflow
  • Removed kma submodule
  • Updated finder submodules (virulencefinder_db, resfinder_db, pointfinder_db, serotypefinder_db)
  • Updated resfinder version
  • Changed memory allowance for hostile
  • Updated docs regarding updating finder dbs
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