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CHANGELOG.md

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genomic-medicine-sweden/jasen: Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[Unreleased]

Added

  • 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

Fixed

  • 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([])

Changed

  • 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 PRP to version 0.11.1

[0.9.0]

Added

  • Added long-read test data (S. aureus)
  • Added samplelist_nanopore.csv for running long-read test data
  • Added location of documentation to README
  • Added cdmDir to config
  • Added process for adding IGV annotation tracks with PRP.
  • Updated how mycobacterium_tuberculosis workflow adds IGV annotation tracks.

Fixed

  • Fixed --qc argument filepath to be full filepath to output
  • Fixed tbprofiler url in container Makefile
  • Fixed TB installation steps in main Makefile

Changed

  • Updated TbProfiler to version 6.3
  • Updated PRP to version 0.10.0
  • Removed delly annotation
  • Updated vcf args in prp module

[0.8.0]

Added

  • Added ShigaPass
  • Added mlstBlastDb to mlst
  • Added full path for bam and vcf filepaths
  • Added bam and bai to bonsai input for staphylococcus_aureus, escherichia_coli & klebsiella_pneumoniae
  • Added bamDir and vcfDir to config params
  • Added run bwa_mem from only when profile is not mycobacterium_tuberculosis
  • Added sample_name to get_seqrun_meta
  • Automatically publish the pipeline documentation to read the docs.

Fixed

  • ShigaPass URL fixed
  • Fixed qc channel regarding mycobacterium_tuberculosis
  • Fixed bwa output file bug and stub
  • Fixed README re jasentool cmds
  • Fixed get_seqrun_meta if statements
  • Fixed getting some software versions
  • Fixed tb workflow bug

Changed

  • Fixed output format for tbprofiler
  • Removed samtools_sort_ref from configs
  • Changed --symlink_dir arg for prp
  • Changed sampleName to sampleID
  • Updated flye, freebayes, mask, medaka, post_align_qc, skesa & spades output filenames
  • Updated bonsai-prp to v0.9.3
  • Updated the pipeline documentation.
  • Removed sudo from make (deprecated)
  • Updated NGP config for new hardware
  • Updated tbprofiler memory allocation

[0.7.0]

Added

  • Added two modules for assembly of long-read Nanopore data: Flye and Medaka
  • Added referenceGenome to prp create-bonsai-input
  • created .fai files from all genomes in Makefile
  • Added samtools_sort_ref to tb workflow with 4GB memory (may need more)
  • Added more cpus to tbprofiler

Fixed

  • Added nanopore to all workflows
  • Sort and index tbprofiler bam output

Changed

  • Updated saureus genome from NC_002951.2 to GCF_000012045.1
  • Updated ecoli genome from NC_000913.3 to GCF_000005845.2
  • Updated mtuberculosis genome from NC_000962.3 to GCF_000195955.2
  • Updated kpneumoniae genome from NC_016845.1 to GCF_000240185.1
  • Updated tbprofiler to v6.2.0
  • Updated download_ncbi.py to include .gff files
  • Updated bonsai-prp to v0.8.3
  • Removed FoHM variant duplicates

[0.6.0]

Added

  • Added converged_who_fohm_tbdb.csv
  • Added guide to create tbdb
  • Added sequencing_run and lims_id to output
  • Added devMode flag
  • Added lims_id & sequencing_run to meta module
  • Added annotate_delly module
  • Added prp versions
  • Added how-to guide on how to create bed file, bgzipped format and index for annotate_delly input
  • Prepare general Makefile for incorporation of tbprofiler v6.1.0 to auto create above files and create new tbdb
  • Add create_yaml module for upload to bonsai

Fixed

  • Args for cdm

Changed

  • Run with converged/merged db
  • Publish bam & bai from tbprofiler
  • cronCopy set true in hopper config
  • bonsai-prp version upgraded from v0.5.0 to v0.6.0
  • Renamed nextflow.hopper.config to nextflow.dev.config for hopper development
  • bonsai-prp version upgraded from v0.6.0 to v0.7.0
  • bonsai-prp version upgraded from v0.7.0 to v0.7.1
  • Changed blastDb to pubMlstDb re mlst

[0.5.0]

Added

  • Added a GitHub workflow to run a basic CI pipeline.
  • Build prp as singularity image from dockerhub in Makefile
  • Chewbacca and virulencefinder sif fetched from galaxyproject
  • Added species to amrfinderplus
  • Added getSpeciesTaxonName to amrfinderplus
  • Add serotypefinder to Makefiles, workflows, modules & configs

Fixed

  • Fixed config not pointing to the new lowercase repo name: jasen (instead of JASEN)

Changed

  • Changed to use full file paths in include statements for better navigation in text editors.
  • Upgraded the Skesa (container) to v2.5.1 to fix ownership issue with /tmp folder
  • Changed pythonScripts.sif filename to bonsai-prp.sif
  • Postalignqc added to prp and move to prp module
  • Makefile converts bonsai-prp from docker image to singularity
  • Makefile pulls all containers from online respositories
  • Configs can also pull images from galaxy project or dockerhub
  • Move post_align_qc to prp module

[0.4.0]

Added

  • Added tbdb as a submodule.
  • Downloaded new catalogue from WHO and convert to csv required for tbdb creation using jasentool.
  • DB creation included using Makefile.
  • Updated configs.
  • Updated workflows/mycobacterium_tuberculosis.nf.
  • Update TBProfiler version to v5.0.1.
  • Publish delly output when running tbprofiler.
  • Remove Tbprofiler run using WHO database until TBProfiler issue #313 resolved.

Fixed

Changed

  • Updated PRP to verion 0.3.0

0.3.0

Added

  • E.coli STX typing using Virulencefinder

Changed

  • Moved PRP to seperate repo
  • Updated PRP to v0.2.0

0.2.0

Added

  • The pipeline now supports IonTorrent input data
  • Both Single-End and Paired-End input is now supported
  • Test suite is entirely containerised within Singularity
  • Versions of all used software is conveniently written into a single file
  • Assemblies are automatically cleaned up
  • AMRFinder has replaced ARIBA
  • SKESA de novo assembly added
  • Readme contains simple usage instructions and more detailed breakdown of components
  • External nextflow-modules are now fully integrated

Changed

  • Extensive Nextflow code refactoring
  • Memory and CPU usage defaults optimised for all modules
  • Optimisation of module invocations to reduce overhead
  • PRP identifiers updated
  • Updated all utilised databases to latest version
  • Various publishDir updates

Fixed

  • Resolved multiple BLAST database referencing errors
  • Singularity images are now umasked properly
  • Minimum recommended RAM expanded to avoid runtime crashes
  • Fixed 'failed to publish file' error
  • MLST PRP input issues fixed
  • Metadata is now properly saved

Removed

  • Removed legacy modules (notably ARIBA)
  • Reduction to only two software requirements; Singularity and Nextflow

0.1.0