Releases | Open Source Science

v3.2.0 bactopia/bactopia "Black Bulls" 2025/03/21

"Black Bulls" is related to the best magic squad in Black Clover my kids currently watching

`Added`

Bactopia Tools (bactopia --wf <NAME>)
- checkm2 - Rapid assessment of genome bin quality using machine learning @maxlcummins
- sylph - taxonomic profiling and genome querying for meta-genomic samples
teton now outputs a bactopia sample sheet with species and genome size filled out
- sizemeup uses the bracken output to determine genome size
more metrics and helper text at end of runs
snippy use a local directory for --tmpdir
bactopia atb-downloader to download ATB assemblies by BioSample, TaxID, or species
pangenome add SNP dists for both masked and unmasked alignments
within task clean up to help reduce work directory size
- gtdb: add --gtdb_keep_msa to keep GTDB MSA files, otherwise remove
- kraken2: replace --remove_filtered_reads with --keep_filtered_reads to keep classified and unclassified reads
- ncbigenomedownload: add --keep_genomes to publish downloaded genomes, default leave in work directory
  - this also affects Prokka annotations in the pangenome workflow
- snippy: add --snippy_remove_bam to remove BAM files after variant calling
support for custom databases in emmtyper @maxlcummins
bump program versions in modules
- amrfinderplus: 3.12.8 -> 4.0.19
- bactopia-teton: 1.0.2 -> 1.1.1
- bakta: 1.9.4 -> 1.11.0
- busco: 5.7.1 -> 5.8.2
- csvtk: 0.27.2 -> 0.31.0
- gubbins: 3.3.5 -> 3.4
- iqtree: 2.2.2.7 -> 2.3.6
- kleborate: 3.0.9 -> 3.1.3
- multiqc: 1.24.1 -> 1.27.1
- panaroo: 1.5.0 -> 1.5.1
- quast: 5.2.0 -> 5.3.0
- sister: 1.1.2 -> 1.1.3
- sylph: 0.6.1 -> 0.8.0
- tbprofiler: 6.3.0 -> 6.6.2

`Fixed`

debugging print in functions.nf
fixed params.max_retry in local profiles
nextflow.config accessing param vals before they are set
removed lingering task.ext which were not used
replace --singularity_cache_dir with --singularity_cache to match bactopia download
gamma not checking for --gamma_db at runtime
tests using single protein (typo in file name config)
pangenome mislabeling pangenome tool used (was using the correct tool)
downloaded genomes added to --bactopia directory for pangenome
useless use of options.btype ?: in modules (it didn't actually do anything because options.btype was always empty)
version capture in dragonflye and mlst
mismatch in defensefinder conda and container versions
kraken-bracken-summary.py failing with 0 unclassified reads @maxlcummins

- Nextflow
Published by rpetit3 11 months ago

v3.1.0 bactopia/bactopia "Dance Powder" 2024/09/22

"Dance Powder" is related to the Alabasta arc in One Piece which my kids currently on

`Added`

Named Workflows
- clean-yer-reads - Use Bactopia's read QC steps to Clean-Yer-Reads
  - Use clean-yer-reads, cyr or bactopia --wf cleanyerreads
- teton - Host removal and taxon classification with estimated abundances
  - Use teton or bactopia --wf teton
Bactopia Tools (bactopia --wf <NAME>)
- clermontyping - Clermont's Escherichia phylogrouping
- defensefinder - Systematic search of all known anti-phage systems
- sccmec - SCCmec typing of Staphylococcus aureus genomes
- scrubber - Remove human reads from FASTQ files
  - screen human reads with kraken2 (against human pangenome) or sra-human-scrubber
- shigapass - Predict Shigella serotypes and differentiate Shigella, EIEC and non-Shigella/EIEC
full support of config files from nf-core/configs
- no longer prints efficiency for standard, docker, and singularity profiles
- now required non-integer values for --max_time (e.g. 4.h) and --max_memory (e.g. 8.GB)
- always import base.config
amrfinderplus by combining results from genes, proteins and gff (coordinates)
--amrfinder_db and --mlst_db to specify custom databases
mlst and amrfinder databases can now be either a tarball or directory
pangenome tool now uses panaroo as the default pangenome tool
file with reference name and samples included for snippy run
snippy can now use --accession to download a genbank file from NCBI
replaced staphopiasccmec with sccmec in staphtyper
bump program versions in modules
- abritamr: 1.0.17 -> 1.0.19
- bakta: 1.9.3 -> 1.9.4
- blast: 2.15.0 -> 2.16.0
- busco: 5.7.0 -> 5.7.1
- checkm: 1.2.2 -> 1.2.3
- defensefinder: 1.2.2 -> 1.3.0
- gtdbtk: 2.3.2 -> 2.4.0
- hicap: 1.0.3 -> 1.0.4 (@MartinVad)
- kleborate: 2.3.2 -> 3.0.9
- mobsuite: 3.1.8 -> 3.1.9
- panaroo: 1.4.2 -> 1.5.0
- pasty: 1.0.3 -> 2.2.1
- pbptyper: 1.0.4 -> 2.0.0
- seqsero2: 1.2.1 -> 1.3.1
- stecfinder: 1.1.1 -> 1.21.2
- tbprofiler: 6.1.0 -> 6.3.0

`Fixed`

missing schema for clean-yer-reads and teton
pinning of bioperl in prokka module with strict channel priority
use --infile-list with csvtk concat to support 10k+ inputs
pangenome when Bakta GFF (*.gff3) files are provided
missing file export in gubbins
writing to non-default values for --bactopia
--include file on cloud storage (@rwilliams)
import of ONT reads over illumina reads in certain bactopia tools (e.g. snippy) (Thanks D2)
bactopia/datasets envs not being build by bactopia download
snippy puts files in subdirectory based on reference name
removed pneumocat from Merlin as it doesn't gracefully fail on negative results
all the tests
typo in bactopia-tools.nf (thank you! @pvanheus)

`Enhancements to OSS`

pinn macsyfinder version in defense-finder bioconda/bioconda-recipes#46824
add recipe for camlhmp bioconda/bioconda-recipes#47453
add recipe for sccmec bioconda/bioconda-recipes#47600
update recipe for genotyphi bioconda/bioconda-recipes#47664
disable phone home snpeff bioconda/bioconda-recipes#48007
clermontyping use share folder bioconda/bioconda-recipes#49372
add recipe for scrubby bioconda/bioconda-recipes#49373
rebuild pasty bioconda/bioconda-recipes#50068

- Nextflow
Published by rpetit3 over 1 year ago

v3.0.1 bactopia/bactopia "That's My Girl" - 2024/03/25

`Added`

Updated bactopia-assembler to include updated Medaka models
profile for arcc_hawk
TB Profiler results are now merged with collate command
sample name to plasmidfinder results
support config files from nf-core/configs
updated AMRFinder+ database for v3.12.8
bump program versions in modules
- abritamr: 1.0.14 -> 1.0.17
- bactopia-assembler: 1.0.3 -> 1.0.4
- bactopia-teton: 1.0.1 -> 1.0.2
- bactopia-variants: 1.0.1 -> 1.0.2
- bakta: 1.8.2 -> 1.9.3
- blast: 2.14.1 -> 2.15.0
- busco: 5.5.0 -> 5.7.0
- gubbins: 3.3.0 -> 3.3.4
- multiqc: 1.15 -> 1.21
- mashtree: 1.4.5 -> 1.4.6
- mykrobe: 0.12.2 -> 0.13.0
- ncbi-amrfinderplus: 3.11.18 -> 3.12.8
- panaroo: 1.3.3 -> 1.4.2
- rgi: 6.0.2 -> 6.0.3
- sistr: 1.1.1 -> 1.1.2
- stecfinder: 1.1.0 -> 1.1.1
- tbprofiler: 5.0.0 -> 6.1.0

`Fixed`

variable name in sketcher module
--para-off not correctly implemented in PIRATE module
extra space in RGI container image name
sourmash version STDERR not parsed out
FASTQC writing to /tmp dir on HPC when non-readable
abricate and ariba not using output subdirectory
nextflow tower typos @iferres
phispy not working with Bakta genbank files
missed check of --download_bakta param in main workflow
quast not working when estimated genome size is 0
abricate now gets database subdirectories

`Enhancements to OSS`

fix amrfinderplus pinning in abritamr bioconda/bioconda-recipes#46714
adjust python pinning in gubbins bioconda/bioconda-recipes#46713
fix issue with sistr container bioconda/bioconda-recipes#46712
update rgi pinning for pyrodigal bioconda/bioconda-recipes#46669
pin tabix version in snippy bioconda/bioconda-recipes#46458

- Nextflow
Published by rpetit3 almost 2 years ago

bactopia - v3.0.0

https://github.com/bactopia/bactopia/assets/5334269/23c0314e-ffc8-424b-ac6e-04f9cdf8fb80

v3.0.0 bactopia/bactopia "Black Cat and Brown Dog" - 2023/09/11

`Added`

Bactopia Tools (bactopia --wf <NAME>)
- abritamr - A NATA accredited tool for AMR detection
- blastn - Search against nucleotide BLAST databases using nucleotide queries
- blastp - Search against protein BLAST databases using protein queries
- blastx - Search against protein BLAST databases using translated nucleotide queries
- bracken - Taxonomic classification and species abundance estimation of sequence reads
- btyper3 - Taxonomic classification of Bacillus cereus group isolates
- midas - Estimate bacterial species abundances from FASTQ files
- quast - Assess the quality of assembled contigs
- phispy - Predict prophages in bacterial genomes
- pneumocat - Assign capsular type to Streptococcus pneumoniae from sequence reads
- sra-human-scrubber - Scrub human reads from FASTQ files
- stecfinder - Serotyping Shigella toxin producing Escherichia coli genomes
- tblastn - Search against translated nucleotide BLAST databases using protein queries
- tblastx - Search against translated nucleotide BLAST databases using translated nucleotide queries
per-release databases for amrfinderplus and mlst
new directory structure for outputs
Renamed --R1, --R2, and --SE to --r1, --r2, and --se
--ont now accepts a FASTQ file
GitHub Action to build environments
fastp is default read cleaner, can use previous methods with --use_bbmap
ability to use a BED file to mask regions in snippy-core
--save_sketches to save Mash sketches created during mashtree run5
Porechop is now optional (--use_porechop)
unified publishDir across modules
download datasets using storeDir
- BACTOPIA:DATASETS
- ariba
- sra-human-scrubber
bump program versions in modules
- bakta: 1.6.0 -> 1.8.2
- blast: 2.11.0 -> 2.14.1
- busco: 5.4.3 -> 5.5.0
- csktk: 0.25.0 -> 0.27.2
- eggnog-mapper: 2.1.9 -> 2.1.12
- genotyphi: 1.9.1 -> 2.0
- gtdbtk: 2.1.1 -> 2.3.2
- gubbins: 3.2.1 -> 3.3
- iqtree: 2.2.0.3 -> 2.2.2.7
- fastani: 1.33 -> 1.34
- mashtree: 1.2.0 -> 1.4.5
- mob_suite: 3.1.0 -> 3.1.7
- multiqc: 1.11 -> 1.15
- mykrobe: 0.12.0 -> 0.12.2
- ncbi-amrfinderplus: 3.10.45 -> 3.11.18
- ncbi-genome-download: 0.3.1 -> 0.3.3
- panaroo: 1.3.0 -> 1.3.3
- pasty: 1.0.0 -> 1.0.3
- phyloflash: 3.4 -> 3.4.2
- rgi: 6.0.1 -> 6.0.2
- shigatyper: 2.0.3 -> 2.0.5
- shigeifinder: 1.3.2 -> 1.3.5
- tbprofiler: 4.4.0 -> 5.0.0

`Fixed`

All modules correctly initiate params.options
OpenJDK java cpuset warning message (@idolawoye)
Broken badges in README.md
Pinned GSL to v2.6
symlink in amrfinder+ update (bactopia datasets)
hardcoded --plus in amrfinderplus_run
tests for new directory structure
--nanohq not being properly passed to dragonflye

`Removed`

Bactopia Steps
- ANNOTATE_GENOME - now handled by prokka or bakta
- ANTIMICROBIAL_RESISTANCE - now handled by amrfinderplus
- CALL_VARIANTS - now handled by snippy
- SEQUENCE_TYPE - now handled by mlst
bactopia datasets is now incorporated into bactopia
Conda/Containers for all bactopia-main steps
custom process labels, for generic nf-core process labels

`Enhancements to OSS`

add module for midas nf-core/modules#2696
add modules for sra-human-scrubber nf-core/modules#2694
add module for stecfinder nf-core/modules#2702
update midas pinnings to match docs bioconda/bioconda-recipes#38566
add missing scripts to MLST bioconda/bioconda-recipes#38826
fix GTDB-Tk container bioconda/bioconda-recipes#40333
patch ncbi-genome-download bioconda-recipes#41640
add module for pneumocat nf-core/modules#3592
add module for abritamr/run nf-core/modules#3725
fix hostrange() missing 1 required positional argument: 'database_directory' phac-nml/mob-suite#149
add module for btyper3 nf-core/modules#3817

- Nextflow
Published by rpetit3 over 2 years ago

v2.2.0 bactopia/bactopia "Tornado Tempo" - 2022/11/28

`Added`

--dragonflye_opts to pass additional params to dragonflye
--use_fastp to use fastp for QCing reads
bactopia datasets no longer depends on ariba
--skip_spell_check in bactopia datasets
updated organisms available from PubMLST
custom profile for wsvl
updated citations
use mambaforge for docker builds
Support tarball inputs for large databases
Bactopia Tools (bactopia --wf <NAME>)
- pasty - in silico serogrouping of Pseudomonas aeruginosa isolates
- pbptyper - In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies
- shigeifinder - Serotyping Shigella and EIEC assemblies
bump program versions in modules
- bakta -> 1.5.1
- bbmap -> 39.01
- checkm-genome -> 1.2.2
- csvtk -> 0.25.0
- dragonflye -> 1.0.13
- eggnog-mapper -> 2.1.9
- fastani -> 1.33
- fastq-scan -> 1.0.1
- gamma -> 2.2
- gtdbtk -> 2.1.1
- iqtree -> 2.2.0.3
- kleborate -> 2.2.0
- mlst -> 2.23.0
- mob_suite -> 3.1.0
- mykrobe -> 0.12.0
- nanoplot -> 1.40.2
- ncbi-amrfinderplus-> 3.10.45
- panaroo -> 1.3.0
- pirate -> 1.0.5
- rasusa -> 0.7.0
- rgi -> 6.0.1
- shigatyper -> 2.0.3
- snpeff -> 5.1
- sourmash -> 4.5.0
- sra-tools -> 3.0.0
- tb-profiler -> 4.4.0

`Fixed`

respect short polish hybrid assembly requests
missing variable in bakta_download module
restructure to match nf-core/modules
compatibility with Nextflow >=22.10
separate versions for Linux and OSX in assemble_genomes
bactopia datasets error messages switched to warnings

`Enhancements to OSS`

bump Bakta to 1.5.0 nf-core/modules#2000
add recipe for pasty bioconda/bioconda-recipes#35930
add recipe for pbptyper bioconda/bioconda-recipes#36222
add module for pasty nf-core/modules#2003
add module for pbptyper nf-core/modules#2005
add module for shigeifinder nf-core/modules#2523

- Nextflow
Published by rpetit3 about 3 years ago

v2.1.1 bactopia/bactopia "Dragon Twister" - 2022/07/09

`Added`

Add Panaroo to the pangenome Bactopia Tools
Add genotyphi and seroba to Merlin
bump fastq-dl to v1.1.1
Bactopia Tools (bactopia --wf <NAME>)
- busco - Assembly completeness based on evolutionarily informed expectations
- genotyphi - Salmonella Typhi genotyping with Mykrobe outputs
- gubbins - Rapid phylogenetic analysis of recombinant bacterial sequences
- mcroni - Sequence variation in mobilized colistin resistance (mcr-1) genes
- mykrobe - Antimicrobial resistance detection for specific species
- panaroo - Pipeline for pangenome investigations
- plasmidfinder - Plasmid identification from assemblies
- seroba - Serotyping of Streptococcus pneumoniae from sequence reads
- snippy - Rapid variant calling from Illumina sequence reads with optional core-SNP phylogeny

`Fixed`

improve GTDB db handling
Properly capture assemblies with 0
user provided adapters and phix fastas
--available_datasets in the bactopia datasets
name collisions in the Ariba Bactopia Tool
bare double-quotes in Ariba reports
updated tests for new version

`Enhancements to OSS`

Add database to Seroba recipe bioconda/bioconda-recipes#35378
Update ariba dependencies bioconda/bioconda-recipes#35383
patch pymummer recipe bioconda/bioconda-recipes#35379
Update PlasmidFinder for better container support bioconda/bioconda-recipes#35314
add module for ariba nf-core/modules#1731
add module for mcroni nf-core/modules#1750
add module for Mykrobe and GenoTyphi nf-core/modules#1731
add module for plasmidfinder nf-core/modules#1773
add module for Seroba nf-core/modules#1731
add module for snippy/core nf-core/modules#1855
let tempfile determine temp dir location sanger-pathogens/seroba#68
allow the user to specify temp dir or use the system default sanger-pathogens/pymummer#36

- Nextflow
Published by rpetit3 over 3 years ago

v2.1.0 bactopia/bactopia "Silver Mist" - 2022/06/08

`Added`

--use_bakta to replace Prokka with Bakta in main workflow
Split Bakta into two processes download and run
added shigatyper to Merlin
custom profile for arcc
bactopia prepare error message when nothing found, and --examples for example use cases
renamed --fastqs to --samples to better reflect its usage (fastqs and assemblies)
add --check_samples to validate user generated FOFNs
--short_polish for short read polishing for long-read assemblies
Moved Ariba to Bactopia Tools
bump versions in Bactopia envs
bump Bactopia Tool versions
- amrfinder+ version to 3.10.30
- gtdb version to 2.1.0
- mlst version to 2.22.0
Bactopia Tools (bactopia --wf <NAME>)
- ariba - Gene identification by local assemblies
- gamma - Identification, classification, and annotation of translated gene matches
- shigatyper: Shigella serotype from Illumina or Oxford Nanopore reads

`Fixed`

@nickjhathaway Fixed assemblylevel in bactopia datasets and auto `callvariants`
bactopia search now supports ONT reads
vcf-annotator unable to write to /dev/stdout
typo in bactopia download when using singularity
bactopia download will not rebuild envs its already built in a run
--include_genus with bactopia datasets now works with multiple samples
Parameters to copy optional species-specific files in bactopia datasets
Don't use AUTO for IQ-TREE cpus
gtdb download working again
empty FASTQs after adapter and phix removal
low read count error for ONT samples
Removed sequence_type environment

- Nextflow
Published by rpetit3 over 3 years ago

v2.0.3 bactopia/bactopia "King Cobra" - 2022/03/23

`Added`

logo and new metro style workflow
added test profile for easy testing
mashdist now outputs a merged TSV
print missing required parameters in Bactopia Tools
bump bakta to v1.4.0

`Fixed`

typo in bakta subworkflow
ismapper not available in bactopia-tools.nf
kraken2 not available in bactopia-tools.nf
Traits file being required for pangenome
mashtree module not collecting all FASTA
tests for ISMapper

Full Changelog: https://github.com/bactopia/bactopia/compare/v2.0.2...v2.0.3

- Nextflow
Published by rpetit3 almost 4 years ago

v2.0.2 bactopia/bactopia "Black Mamba" - 2022/02/22

`Added`

bactopia download which merges the bactopia build and bactopia pull commands
modules can now use prebuilt envs
--available_species to print the species in a bactopia dataset
--bbduk_opts to fine tune bbduk
set quay as default docker registry
Let Nextflow handle stdout and stderr
added hpsuissero, legsta, sistr, ssuissero to Merlin
Bactopia Tools (bactopia --wf <NAME>)
- amrfinderplus: Identify antimicrobial resistance in genes or proteins
- abricate: Mass screening of contigs for antimicrobial and virulence genes
- checkm: Assess the assembly quality of your samples
- hpsuissero: Serotype prediction of Haemophilus parasuis assemblies
- kraken2: Taxonomic classification of sequence reads
- legsta: Typing of Legionella pneumophila assemblies
- mlst: Scan contig files against PubMLST typing schemes
- mobsuite: Reconstruct and annotate plasmids in bacterial assemblies
- rgi: Predict antibiotic resistance from assemblies
- sistr: Serovar prediction of Salmonella assemblies
- ssuissero: Serotype prediction of Streptococcus suis assemblies

`Fixed`

toInteger on null genome size
Index out of bounds in mlst-blast.py (caused by non allele columns)
FOFN will fail if sample name is null
improve available workflow logic
PIRATE not exporting genepresenceabsence.csv correctly
channel imports for scoary workflow
argument type mismatch when using --use_roary
missing channel when agrvate not ran as staphtyper
float required options to the top when missing
broken tests due to changes
bactopia datasets including hidden directories
Bioperl pinnings for prokka and pirate

- Nextflow
Published by rpetit3 about 4 years ago

v2.0.1 bactopia/bactopia "Red Roc" - 2022/01/06

`Added`

Merlin for auto selection of species-specific tools based
--ask_merlin to execute the Merlin subworkflow in Bactopia
Schema compatible with NF-Tower
--skip_qc_plots to skip FastQC and Nanoplot
Disable CheckM by default, must use --run_checkm
--cluster_opts for passing additional options to SLURM
inclusion of local files (assembly, gff) in some subworkflows
workflow for dev conda builds
all subworkflows can be imported on other workflows
Bactopia Tools (bactopia --wf <NAME>)
- gtdb: Identify marker genes and assign taxonomic classifications
- mashdist: Calculate Mash distances between sequences
- merlin: MinmER assisted species-specific bactopia tool seLectIoN

`Fixed`

Resource over allocation for java related programs (-Xmx)
ordering of skipped steps when --datasets not used
logic in container selection for nf-core modules
channel manipulation in ncbigenomedownload
missing logic for fastani
version captures in subworkflows
spell check for species with [ or ] in their names
version outputs for Staphtyper subworkflow
use process names in version.yml
CSVTK_CONCAT empty channels
options.suffix now used as prefix in modules

- Nextflow
Published by rpetit3 about 4 years ago

v2.0.0 bactopia/bactopia "Red Hawk" - 2021/12/05

With Bactopia v2 comes a lot of changes! I would like to extend a huge thanks to Davi Marcon and Abhinav Sharma for their work initially converting Bactopia to DSL2. Your efforts were the momentum I needed to get the ball rolling on Bactopia v2. Thank you very much for taking your time to make such a siginificant contribution!

`Added`

support for Nanopore reads
staphopia as a named pipeline (alias for bactopia --wf staphopia) for S. aureus genomes
bactopia/bactopia-tests repo with test data
walkthrough for testing
bactopia-datasets/staphylococcus_aureus repo with curatated S. aureus datasets
per-module testing via pytest (100+ tests and 7000+ outputs tested)
per-module meta.yml and params.json for auto-building docs site
framefork for adding new Bactopia Tools
19 total Bactopia Tools (bactopia --wf <NAME>)
- Subworkflows (3)
  - eggnog: Functional annotation of proteins using orthologous groups and phylogenies
  - pangenome: Pangenome analysis with optional core-genome phylogeny
  - staphtyper: Determine the agr, spa and SCCmec types for Staphylococcus aureus genomes
- Modules (16):
  - agrvate: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.
  - bakta: Rapid annotation of bacterial genomes and plasmids
  - ectyper: In-silico prediction of Escherichia coli serotype
  - emmtyper: emm-typing of Streptococcus pyogenes assemblies
  - fastani: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
  - hicap: Identify cap locus serotype and structure in your Haemophilus influenzae assemblies
  - ismapper: Identify insertion sites positions in bacterial genomes
  - kleborate: Screening Klebsiella genome assemblies for MLST, sub-species, and other related genes of interest
  - lissero: Serogroup typing prediction for Listeria monocytogenes
  - mashtree: Quickly create a tree using Mash distances
  - meningotype: Serotyping of Neisseria meningitidis
  - ngmaster: Multi-antigen sequence typing for Neisseria gonorrhoeae
  - seqsero2: Salmonella serotype prediction from reads or assemblies
  - spatyper: Computational method for finding spa types in Staphylococcus aureus
  - staphopiasccmec: Primer based SCCmec typing of Staphylococcus aureus genomes
  - tbprofiler: Detect resistance and lineages of Mycobacterium tuberculosis genomes
Use mamba instead of conda for env building
Reduced total Conda envs/Docker containers down to 7 (previously 12 not including bactopia tools)
default to compressed outputs (--skip_compression to output uncompressed outputs)
Tutorial outputs made available
update github actions

`Fixed`

Cache issue causing -resume to fail
amrfinder+ database not compatible error
incorrectly parsed system memory

Adapted from `nf-core`

nf-core pytest setup
nf-core/modules for bactopia tools
- Bactopia v2 release contributed 20+ modules to nf-core/modules
nf-core/tools arg parser
- adapted to import params and usage based on config file

Process Consolidation

makeblastdb -> assemble_genome
call_variants, download_reference -> call_variants
fastq_status, estiamte_genome_size -> gather_samples
count_31mers -> minmer_sketch

`Removed`

bactopia tools -> Handled by Nextflow now (bactopia --wf <NAME>)
bactopia versions -> Program versions are output ever run now.

- Nextflow
Published by rpetit3 about 4 years ago

bactopia - v1.7.1

v1.7.1 bactopia/bactopia "Shellbuster" - 2021/06/04

`Added`

bumped GTDB to v1.5.0
added soft ulimit for staph-typer

`Fixed`

Matched PIRATE's parameter syntax for the tools
staph-typer now uses GetBaseName

'Removed'

PLSDB references in bactopia datasets

- Nextflow
Published by rpetit3 over 4 years ago

bactopia - v1.7.0

v1.7.0 bactopia/bactopia "Chocobo Wand" - 2021/04/27

`Added`

Bactopia Tool staph_typer for agr, spa, and sccmec typing
--min_coverage parameter to filter based on min coverage

'Removed'

plasmid_blast no longer apart of main workflow

- Nextflow
Published by rpetit3 almost 5 years ago

bactopia - v1.6.5

v1.6.5 bactopia/bactopia "Z's Trident" - 2021/03/30

`Added`

version pins to process envs

`Fixed`

syntax for sourmash 4.0

- Nextflow
Published by rpetit3 almost 5 years ago

bactopia - v1.6.4

v1.6.4 bactopia/bactopia "Trident +1" - 2021/03/27

`Added`

added Python3.6+ to all environments

- Nextflow
Published by rpetit3 almost 5 years ago

bactopia - v1.6.3

v1.6.3 bactopia/bactopia "Trident" - 2021/03/25

`Added`

extra fields to mlst-blast.py outputs
added Python3 to qc_reads environment

`Fixed`

rstrip on empty extra fields in mlst profile
different BLAST+ software versions mismatch
tbb pinnings
--help and --version for bactopia tools

- Nextflow
Published by rpetit3 almost 5 years ago

bactopia - v1.6.2

v1.6.2 bactopia/bactopia "Fuscina" - 2021/03/19

`Added`

inputs are checked to be gzipped (this does not include FOFN)
--skip_amr to skip AMRFinder+ analysis
new bactopia tool for hicap
unicycler can be used for Illumina reads only (--assembler unicycler)

`Fixed`

AMRFinder+ software and database version mismatch
check-fastqs.py syntax errors with prints
ismapper tool processing of include/exclude files

- Nextflow
Published by rpetit3 almost 5 years ago

bactopia - v1.6.1

v1.6.1 bactopia/bactopia "Obelisk" - 2021/02/22

`Fixed`

sample names with "." in them breaking auto variant calling
contig naming incompatible with GenBank

- Nextflow
Published by rpetit3 about 5 years ago

bactopia - v1.6.0

v1.6.0 bactopia/bactopia "Harpoon" - 2021/01/22

`Added`

bactopia pull to pre-build Singularity images
--singularity_cache parameter to set location of image downloads
--registry to choose Docker registry to use (DockerHub, GitHub, Quay)
--max_downloads sets maximum number of downloads (FASTQ/assembly) allowed at once
--min_time sets the minimum amount of time a job should be given
bactopia search now uses POST requests, and groups accessions into single query
strip HTML from FASTA headers used in BLAST
Dockerfiles now have conda.md5 label to determine if rebuild is necessary
- MD5 is updated in Dockerfile when env is updated
AMRFinder+ database is now provided by bactopia datasets
Parameterized profile (slurm, awsbatch, etc...) variables
bactopia build
- will retry in case of HTTP connection issues
- --include_tool will build Bactopia Tool environments
GitHub Actions
- build Docker containers on new release (or manual trigger)
- test that the Conda environment yamls are still valid
- test bactopia with conda on Linux and OSX
- test bactopia on Linux with Docker and Singularity

`Fixed`

redundant environment version files
failed FASTQ/Assembly downloads no longer stop whole run
--max_retry is honored now
antimicrobial_resistance process honors amrdir variable
change directory antimicrobial_resistance to antimicrobial-resistance
rename check_staging.py to check-staging.py for consistency
Bactopia not producing valid exit code on failure

`Removed`

--containerPath variable is replaced by --singularity_cache
Native Singularity recipes, will now convert Docker to Singularity
docs are now on bactopia.github.io repo

- Nextflow
Published by rpetit3 about 5 years ago

bactopia - v1.5.6

v1.5.6 bactopia/bactopia "Metal Slime Earring" - 2021/01/13

`Added`

tweaks to the CI (via GitHub Actions)
docker containers use quay.io now
docker containers now use conda-pack
--nfconfig will skip the conda environment build step
input accessions are checked to be Assembly or Experiment accessions
improved version increment script

`Fixed`

phyloflash and download_reference environment errors
environment path in Bactopia Tools Dockerfile and Singularity recipes
moved version from conda yaml to conda version file
streamlined Docker recipes
undefined --ftp_only message
typo in singularity profile
stderr logged to file is also printed to screen
qc_reads memory used now determined by base config

- Nextflow
Published by rpetit3 about 5 years ago

bactopia - v1.5.5

v1.5.5 bactopia/bactopia "Avenger's Earring" - 2021/01/04

`Added`

--prefix option for bactopia prepare
date is included in bactopia summary output

`Fixed`

removed usage personal (rpetit3) conda channel
- aspera connect no longer supported
- shovill-se is now used from Bioconda
updated conda environments (phyloflash broken)

- Nextflow
Published by rpetit3 about 5 years ago

bactopia - v1.5.4

v1.5.4 bactopia/bactopia "Nemesis Earring" - 2020/12/17

`Fixed`

quoted arguments being broken up (e.g. --species "Staphylococcus aureus -> --species Staphylococcus)
mashtree tool failure to download with --accessions
remove ncbi-genome-download header when using --dry-run
undefined name variable in plasmid_blast
custom work dir causing two -w parameters
bactopia search results now contains all (illumina and non-illumina)

- Nextflow
Published by rpetit3 about 5 years ago

bactopia - v1.5.3

v1.5.3 bactopia/bactopia "Morion Earring" - 2020/12/04

`Added`

Changelog moved to docs
recursive search for bactopia prepare
allow multiple FASTQs per sample (FASTQs are merged)

`Fixed`

unable to run bactopia datasets without parameters
PLSDB blast results in invalid JSON format
Error message for unaccepted run_type

- Nextflow
Published by rpetit3 about 5 years ago

bactopia - v1.5.2

v1.5.2 bactopia/bactopia "Physical Earring" - 2020/11/18

`Fixed`

--skip_qc causing "file not found"
qc_reads not honoring FINALBP and FINALREADS checks

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - v1.5.1

v1.5.1 bactopia/bactopia "Astral Earring" - 2020/11/17

`Fixed`

bactopia tools not a valid project name
bactopia tools --cleanup_workdir unrecognized variable

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - v1.5.0 - Versioned Conda envs, bug fixes, improved OSX support.

v1.5.0 bactopia/bactopia "Cassie Earring" - 2020/11/12

`Added`

Conda environments will check if in sync with latest version now
md5sums of all conda envs
Verify species-specific datasets exist
separate work dir for bactopia and bactopia tools
--cleanup_workdir to delete work directory after successful run
default values for bactopia datasets summary.json
Fallback to NCBI Assembly when eUtils is down
Additional pre-process QC checks
OSX/Linux conda envs for Bactopia Tools
Documentation edits and updates
Bactopia and Nextflow versions are now output for logging purposes
option to skip QC step (--skip_qc)
bactopia datasets can now specify assembly level
bactopia tools now use reusable conda envs
bactopia tools for Roary and PIRATE can now include local assemblies

`Fixed`

Warn user if no completed genomes are available
use of --genera for ncbi-genome-download
improved genome_size handling
explicit file passing for AWS Batch
Memory estimates now floored
PLSDB blast not being executed

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - OSX Compatibility, bug fixes

v1.4.11 bactopia/bactopia "Metamorph Ring" - 2020/09/19

`Added`

bactopia build checks if each environment is built before building
Can specify bactopia build to build a specific environment
Removed build numbers in Conda environment yamls
Created separate Conda yamls for Linux and Mac
NCBI assembly accessions will retrieve the most current version (e.g. .1, .2, .3, etc...)

`Fixed`

bactopia datasets trailing whitespace in species names
bactopia datasets random subsample missing specified species when --limit and --include_genus used
GitLab CI OSX compatibility
Adaptive resource allocations
Datasets are checked for existence
Variant calls against references with multiple chromosomes

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - Timestamps, CARD and making directories

v1.4.10 bactopia/bactopia "Jelly Ring" - 2020/08/25

`Added`

card is back as a default Ariba dataset
Added timestamps to versions files

`Fixed`

bactopia search not creating --outdir
gtdb tool not using prefix in outdir naming
pirate tool using pangenome alignment instead of core
Use of scratch causing logs to fail

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - Multiple accessions, endpoint fixes, bugs

v1.4.9 bactopia/bactopia "Toreador's Ring" - 2020/08/23

`Added`

Support for multiple accession
- bactopia search (SRA)
- Bactopia Tools: fastani, mashtree, pirate, roary (Assembly)

`Fixed`

Undefined variable in mapping_query.sh
ENA API endpoint for bactopia search
Updated GTDB-TK to 1.3.0 to support latest downloads
FastANI tool merge_results in no longer a separate step
- ANI is now one-to-many calculations
--reassemble misapplied

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - Squashing bugs and logging it

v1.4.8 bactopia/bactopia "Shikaree Ring" - 2020/08/20

`Added`

Versions are logged for Bactopia
STDOUT/STDERR logs are kept for each sample
- can be skipped using --skip_logs

`Fixed`

Long sample names breaking Prokka annotation
Syntax errors in Bactopia tools
null values being tested as integers
Ariba card and mlst downloads not working
missing parameter in GTDB Bactopia tool

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - Add no cache feature

Quick fix related to https://github.com/bactopia/bactopia/issues/119

v1.4.7 bactopia/bactopia "Serket Ring" - 2020/08/17

`Added`

--no_cache to skip caching ncbi assembly info

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - Adjustments related to public data downloads

v1.4.6 bactopia/bactopia "Astral Ring" - 2020/08/17

`Added`

Option to rebuild conda envs to default location
Updated fastq-dl for sra-toolkit forced interaction workaround

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - Squashing bugs

v1.4.5 bactopia/bactopia "Bomb Queen Ring" - 2020/08/13

`Fixed`

--min_basepairs and --min_reads not being honored

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - Bug fixes

Should fix issues: https://github.com/bactopia/bactopia/issues/116 and https://github.com/bactopia/bactopia/issues/115

v1.4.4 bactopia/bactopia "Vilma's Ring" - 2020/08/13

`Fixed`

annotate_genome name clashes
Updated fastq-dl version to support new ENA API endpoint

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - bactopia subtool bug fixes

Key changes:

Temporarily removed CARD as default Ariba datasets for bactopia datasets.
- See https://github.com/bactopia/bactopia/issues/113 for more details
Added --skip_ariba option for bactopia datasets
bactopia versions and bactopia citations now working again
Typos, because typos

Installation

Conda: conda create -n bactopia -c conda-forge -c bioconda bactopia

Docker: docker pull bactopia/bactopia

Singularity: singularity pull library://rpetit3/bactopia/bactopia

v1.4.3 bactopia/bactopia "Sattva Ring" - 2020/08/13

`Added`

--skip_ariba option in bactopia datasets

`Fixed`

bactopia versions and bactopia citations improper execution
Convert spaces to tabs in citation doc
Corrected CheckM name in program version info file
CARD no longer default Ariba dataset download for bactopia datasets

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - Bug fix for file of accessions

v1.4.2 bactopia/bactopia "Tamas Ring" - 2020/08/10

`Added`

added requirement checks of --accessions in bactopia datasets
improved ENA spell check for species name

`Fixed`

file of accessions not working with bactopia datasets
Dockerfile and Singularity being missed by update-version.sh

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - Pre-train your annotations!

Minor changes here. Most changes were updating citation info for Bactopia (published woohoo!).

You can now pass a Prodigal training file to bactopia datasets which will be used by Prokka during the annotation step.

v1.4.1 bactopia/bactopia "Rajas Ring" - 2020/08/06

`Added`

Links to publication (woohoo!)
Can pass a Prodigal training file to bactopia datasets

`Fixed`

Typos in the Docs
blastprimers now uses blastn and blastgenes uses megablast
validExitStatus deprecation warning

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - More tools, more input options, additional analyses!

Major changes in v1.4.0 of Bactopia!

Some key changes:

New Bactopia Tools (eggNOG-mapper, ISMapper, Mashtree, PIRATE)
Pre-assembled genomes as inputs
Hybrid assembly (Unicycler)
Assembly assessments (QUAST, CheckM)
Many, many more, full details below!

Installation

Conda: conda create -n bactopia -c conda-forge -c bioconda bactopia

Docker: docker pull bactopia/bactopia

Singularity: singularity pull library://rpetit3/bactopia/bactopia

v1.4.0 bactopia/bactopia "Archer's Ring" - 2020/07/01

`Added`

New Bactopia Tools
- eggnog for functional annotation using eggNOG-mapper
- mashtree to create a tree using Mash distances
- pirate to create pangenome using PIRATE
- ismapper for insertion site discovery
- Documentation for new tools and tweaks to existing
BTs roary and pirate can now be run on just completed genomes
Can limit number of completed genomes downloaded where applicable
bactopia datasets can provide list of RefSeq accessions to download
bactopia search can now use BioSample and Run accessions
bactopia search can select a subset of Experiments associated with a BioSample
Support for organisms with multiple MLST schemas
Assembly QC via QUAST and CheckM
Assemblies (local or NCBI Assembly accession) as inputs for Bactopia
Long reads as supplementary to paired end reads for hybrid assembly
Tools versions are locked to the minor version, not the patch

`Fixed`

summary will now determine absolute path of inputs
fastani improved user reference import
went back a version on call_variants openjdk version
all bactopia tools now put nextflow info in the same folder as outputs
Typos in docs
Bactopia Tools now check existence of include and exclude files
Lots more documentation
Updated citations/tools used by Bactopia
Did I mention typos?

`Removed`

ISMapper as part of the main pipeline (its now a tool)
insertion-sequences in bactopia datasets

- Nextflow
Published by rpetit3 over 5 years ago

bactopia - QOL improvements and bug fixes

Installation

Conda: conda create -n bactopia -c conda-forge -c bioconda bactopia

Docker: docker pull bactopia/bactopia

Singularity: singularity pull library://rpetit3/bactopia/bactopia

v1.3.1 bactopia/bactopia "Emperor Hairpin" - 2020/04/20

`Added`

summary tool now gives reason for rank
summary tools now splits failed into exclude and qc-failure
Better documentation on how --cpus works in Nextflow
Efficiency info when executed on standard profile
split blast_query into blast_genes, blast_primers and blast_proteins
mapping_query now creates multifasta of fastas at maps at once then splits per-base coverage into separate files
--nfconfig users can provide their own Nextflow config file
fastani users can provide their own reference now
bactopia versions will print versions for tools used by Bactopia
bactopia citations will print citations for tools and datasets used by Bactopia
bactopia search can filter based on total bases, mean read length, and missing FASTQs
blast queries results are only JSON format for easy parsing later
added --compliant option for Prokka annotation

`Fixed`

build-containers.sh not working with Bactopia Tools
Bactopia Tools container tools missing environment.yml
Typo in fastani usage
Samples with multiple QC errors counted for each error
Incorrect ISMapper version
typo in summary SLURM profile
gtdb Singularity container not mounting path to GTDB database
roary missing rename in containers
blast_query results overwriting one another
build-containers.sh now creates a "latest" tag
bactopia tool roary outputs results based on the given prefix
renamed --addgenes to --nogenes
updated ASA³P citation
Typos in Bactopia Tools docs
Link in README.md

- Nextflow
Published by rpetit3 almost 6 years ago

bactopia - Zenodo archive of Bactopia

This release is to create a Zenodo archive for the Bactopia preprint.

- Nextflow
Published by rpetit3 almost 6 years ago

bactopia - Bactopia Tools - Workflows for comparing all your genomes

Bactopia Tools are a set of predefined workflows to aid in the comparative analyses of your project. Take a look at the Bactopia Tools Documentation to learn more.

v1.3.0 bactopia/bactopia "Leaping Boots" - 2020/02/19

`Added`

bactopia tools (BT) framework
- docs for each tool
- subcommand to execute tools bactopia tools
- fastani - pairwise average nucleotide identity
- gtdb - assigning objective taxonomic classifications
- phyloflash - 16s assembly, alignment and tree
- roary - pan-genome and core genome tree
- summary - summary of results
--include and --exclude to modify which samples used in BT analysis
update-version.sh improvements
can now set how Nextflow publishes outputs (copy, symlink, etc...) via --publish_mode
Warning if output directory already exists and require --force to overwrite
option (--rfam) to turn on ncRNA annotation in Prokka
reduced "README.md" contents, instead point to documentation
Updated acknowledgements and bibtex for citations

`Fixed`

nextflow.config version out of sync
--available_datasets accessing not existent variable
--available_datasets is tested before requiring inputs
Make use of tbl2asn-forever
adjusted how Bactopia is executed, nextflow run no longer pulls from github

- Nextflow
Published by rpetit3 about 6 years ago

bactopia - Bug fixes and better usage of Nextflow pull

v1.2.4 bactopia/bactopia "Rabbit Charm" - 2019/12/20

`Added`

--conda_help to be used for conda build test
--skip_fastq_check to skip check that input FASTQs meet minimum requirements
Undocumented parameters to the usage

`Fixed`

snippy not working with samtools 1.10
NXF_HOME variable is exported to the conda env location
speed of checking if conda environments are built

- Nextflow
Published by rpetit3 about 6 years ago

bactopia - Bug fixes and quality of life improvements!

v1.2.3 bactopia/bactopia "Tropical Punches +1" - 2019/12/19

`Added`

select-references selects latest assembly accession version (BioPython/Entrez)
select-references skips assemblies that have been excluded from RefSeq
test to for paired-end related errors (e.g. different read counts)
--min_genome_size and --max_genome_size parameter for estimated genome sizes
- Check is also made after assembly
update-version.sh improvements
Better genome size estimates using Mash for high and low coverage sequences
Script to update conda environments

`Fixed`

--random_tie_break always true
not using latest assembly accession for ncbi-genome-download
usage of assemblies that have been excluded from RefSeq
allowing PE reads with different read counts to be processed (hint... they fail pretty quickly)
failure to stop analysis of sample with low read counts
coverage reported as 'inf'
references to cgmlst in the setup datasets
non-explicit patterns in publishDir
low coverage/read errors after QC were not put in root dir

- Nextflow
Published by rpetit3 about 6 years ago

bactopia - SRA support, bug fixes, more docs!

v1.2.2 bactopia/bactopia "Tropical Punches" - 2019/10/22

`Added`

Size of "work" directory to the execution summary
User controlled overwrites of existing output files
Check for unknown parameters at runtime
FASTQ downloads from SRA (via fastq-dl and fasterq-dump)
Documentation updates
Script for building containers

`Fixed`

bactopia command now explicitly states which tag to use for Nextflow run
Version info not updated in Dockerfile and Singularity
Duplicated QC'd FASTQs
nextflow: docker "Memory limited without swap" error

`Removed`

cgmlst support in bactopia datasets
setup.py left over from pre-conda config

- Nextflow
Published by rpetit3 over 6 years ago

bactopia - Typos, config changes, conda fixes, bugs squashed

v1.2.1 bactopia/bactopia "Fruit Punches" - 2019/10/17

`Added`

bactopia build to build Conda environments
Version info pulled from nextflow.config
Set default values resource allocations
Documentation on new changes
Automatic building of Conda environments, if none exist
--nfdir to determine where bactopia is being run from

`Fixed`

Neverending typos
--datasets now, not --dataset <-(Typo)
path for outputing Nextflow reports
Typo in antimicrobial_resistance.sh (task.cpus not cpus)
--species is now consistent between bactopia and bactopia datasets
Bug when checking if specific species dataset exists, but no species datasets exist
Cleaned up version update script
Cleaned up usage

`Removed`

--max_cpus ability to limit total cores used, access to config is being deprecated in Nextflow
--max_cpus since it is redudant to --cpus now

- Nextflow
Published by rpetit3 over 6 years ago

bactopia - Singularity, bug fixes, and more docs!

v1.2.0 bactopia/bactopia "Beestinger" - 2019/10/16

`Added`

--compress to compress certain outputs, default uncompressed
Species name check in bactopia datasets
Use requests package instead of urllib3
Added bactopia search to query ENA for list of Illumina accessions
Documentation
- Feedback edits
- Output overview
- Additional program acknowledgements
- bibtex of citations
- missing parameters to usage
- info for --genome_size parameter
- bactopia search usage
- Workflow overview
blastdbcmd compatible seqid to assembly fasta
- allows search for entries with sample name
Mask low coverage regions in consensus (subs only) fasta
Added --dry_run to build conda envs one at a time (prevent parallel issues)
Added Singularity recipes
Added SLURM config

`Fixed`

Neverending typos
bactopia datasets lowercase species names not found in MLST schemas
bactopia version no longer calls nextflow
SEQUENCE_TYPE channel groups FASTQ and assembly
MINMER_QUERY channel groups FASTQ and signature
Ariba MLST always running with --noclean
Bugs related --compress
Reduced size of per-base coverage outputs
Removed -parse_seqids from makeblastdb command, caused blast queries to fail
genomeCoverageBed failing on empty BAM files

`Removed`

--clean_cache function

- Nextflow
Published by rpetit3 over 6 years ago

bactopia - AMR, docs and bugs!

v1.1.0 bactopia/bactopia "Wooden Sword +1" - 2019/09/19

`Added`

NCBI's amrfinder
Dockerfile for main bactopia install
Completed documentation!

`Fixed`

insertion_sequences inputs are not now grouped into single channel
Unintended FASTQ duplication via poor publishDir pattern

- Nextflow
Published by rpetit3 over 6 years ago

bactopia - A more wild Bactopia v1.0.1 has appeared!

After submitting multiple packages to Conda-Forge (executor, property-manager) and Bioconda (ena-dl), Bactopia is now ready for Bioconda submission.

`Added`

README.md documentation
CHANGELOG.md

`Fixed`

callvariantsauto bug fixed
documentation
version numbers

Installation

conda create -n bactopia -c conda-forge -c bioconda bactopia conda activate bactopia bactopia --help

- Nextflow
Published by rpetit3 over 6 years ago

bactopia - A wild Bactopia v1.0.0 has appeared!

The overall Bactopia workflow has been finalized and is "ready" for public use. So, into the wild you go Bactopia!

Please Post an Issue if you run into any problems.

- Nextflow
Published by rpetit3 over 6 years ago

bactopia - Testing for personal conda build

- Nextflow
Published by rpetit3 over 6 years ago

bactopia - Testing for conda install

This release is for conda testing

- Nextflow
Published by rpetit3 almost 7 years ago

Recent Releases of bactopia

bactopia - v3.2.0

v3.2.0 bactopia/bactopia "Black Bulls" 2025/03/21

Added

Fixed

bactopia - v3.1.0

v3.1.0 bactopia/bactopia "Dance Powder" 2024/09/22

Added

Fixed

Enhancements to OSS

bactopia - v3.0.1

v3.0.1 bactopia/bactopia "That's My Girl" - 2024/03/25

Added

Fixed

Enhancements to OSS

bactopia - v3.0.0

v3.0.0 bactopia/bactopia "Black Cat and Brown Dog" - 2023/09/11

Added

Fixed

Removed

Enhancements to OSS

bactopia - v2.2.0

v2.2.0 bactopia/bactopia "Tornado Tempo" - 2022/11/28

Added

Fixed

Enhancements to OSS

bactopia - v2.1.1

v2.1.1 bactopia/bactopia "Dragon Twister" - 2022/07/09

Added

Fixed

Enhancements to OSS

bactopia - v2.1.0

v2.1.0 bactopia/bactopia "Silver Mist" - 2022/06/08

Added

Fixed

bactopia - v2.0.3

v2.0.3 bactopia/bactopia "King Cobra" - 2022/03/23

Added

Fixed

bactopia - v2.0.2

v2.0.2 bactopia/bactopia "Black Mamba" - 2022/02/22

Added

Fixed

bactopia - v2.0.1

v2.0.1 bactopia/bactopia "Red Roc" - 2022/01/06

Added

Fixed

bactopia - v2.0.0

v2.0.0 bactopia/bactopia "Red Hawk" - 2021/12/05

Added

Fixed

Adapted from nf-core

Process Consolidation

Removed

bactopia - v1.7.1

v1.7.1 bactopia/bactopia "Shellbuster" - 2021/06/04

Added

Fixed

'Removed'

bactopia - v1.7.0

v1.7.0 bactopia/bactopia "Chocobo Wand" - 2021/04/27

Added

'Removed'

bactopia - v1.6.5

v1.6.5 bactopia/bactopia "Z's Trident" - 2021/03/30

Added

Fixed

bactopia - v1.6.4

v1.6.4 bactopia/bactopia "Trident +1" - 2021/03/27

Added

bactopia - v1.6.3

v1.6.3 bactopia/bactopia "Trident" - 2021/03/25

Added

Fixed

bactopia - v1.6.2

v1.6.2 bactopia/bactopia "Fuscina" - 2021/03/19

Added

Fixed

bactopia - v1.6.1

v1.6.1 bactopia/bactopia "Obelisk" - 2021/02/22

`Added`

`Fixed`

`Added`

`Fixed`

`Enhancements to OSS`

`Added`

`Fixed`

`Enhancements to OSS`

`Added`

`Fixed`

`Removed`

`Enhancements to OSS`

`Added`

`Fixed`

`Enhancements to OSS`

`Added`

`Fixed`

`Enhancements to OSS`

`Added`

`Fixed`

`Added`

`Fixed`

`Added`

`Fixed`

`Added`

`Fixed`

`Added`

`Fixed`

Adapted from `nf-core`

`Removed`

`Added`

`Fixed`

`Added`

`Added`

`Fixed`

`Added`

`Added`

`Fixed`

`Added`

`Fixed`

`Fixed`

`Added`

`Fixed`

`Removed`

`Added`

`Fixed`

`Added`

`Fixed`

`Fixed`

`Added`

`Fixed`

`Fixed`

`Fixed`

`Added`

`Fixed`

`Added`

`Fixed`

`Added`

`Fixed`

`Added`

`Fixed`

`Added`

`Fixed`

`Added`

`Added`

`Fixed`

`Fixed`

`Added`