v0.9.0

[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

v0.8.0

[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

v0.7.0

[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

v0.6.0

[0.6.0]

Compatible with Bonsai v0.4.1

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

v0.5.0

[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

v0.4.0

[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

v0.3.0

[0.3.0]

Added

• E.coli STX typing using Virulencefinder

Changed

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

Riveting release

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

Fallback release

0.1.0-beta

Update chewbbaca