Bactopia Tool - merlin

MinmER assisted species-specific bactopia tool seLectIoN, or Merlin, uses distances based on the RefSeq sketch downloaded by bactopia datasets to automatically run species-specific tools.

Currently Merlin knows 16 spells for which cover the following:

Genus/Species	Tools
Escherichia / Shigella	ECTyper, ShigaTyper, ShigEiFinder
Haemophilus	hicap, HpsuisSero
Klebsiella	Kleborate
Legionella	legsta
Listeria	LisSero
Mycobacterium	TBProfiler
Neisseria	meningotype, ngmaster
Pseudomonas	pasty
Salmonella	SeqSero2, SISTR
Staphylococcus	AgrVATE, spaTyper, staphopia-sccmec
Streptococcus	emmtyper, pbptyper, SsuisSero

Merlin is avialable as an independent Bactopia Tool, or in the Bactopia with the --ask_merlin parameter. Even better, if you want to force Merlin to execute all species-specific tools (no matter the distance), you can use --full_merlin. Then all the spells will be unleashed!

Example Usage

bactopia --wf merlin \
  --bactopia /path/to/your/bactopia/results  

Output Overview

Below is the default output structure for the merlin tool. Where possible the file descriptions below were modified from a tools description.

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       ├── agrvate
│       │   ├── <SAMPLE_NAME>-agr_gp.tab
│       │   ├── <SAMPLE_NAME>-blastn_log.txt
│       │   ├── <SAMPLE_NAME>-hmm-log.txt
│       │   ├── <SAMPLE_NAME>-hmm.tab
│       │   ├── <SAMPLE_NAME>-summary.tab
│       │   └── logs
│       │       ├── nf-agrvate.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── ectyper
│       │   ├── <SAMPLE_NAME>.tsv
│       │   ├── blast_output_alleles.txt
│       │   └── logs
│       │       ├── ectyper.log
│       │       ├── nf-ectyper.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── emmtyper
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-emmtyper.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── genotyphi
│       │   ├── <SAMPLE_NAME>.csv
│       │   ├── <SAMPLE_NAME>.json
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── genotyphi
│       │       │   ├── nf-genotyphi.{begin,err,log,out,run,sh,trace}
│       │       │   └── versions.yml
│       │       └── mykrobe
│       │           ├── nf-genotyphi.{begin,err,log,out,run,sh,trace}
│       │           └── versions.yml
│       ├── hicap
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-hicap.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── hpsuissero
│       │   ├── <SAMPLE_NAME>_serotyping_res.tsv
│       │   └── logs
│       │       ├── nf-hpsuissero.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── kleborate
│       │   ├── <SAMPLE_NAME>.results.txt
│       │   └── logs
│       │       ├── nf-kleborate.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── legsta
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-legsta.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── mashdist
│       │   └── merlin
│       │       ├── <SAMPLE_NAME>-dist.txt
│       │       └── logs
│       │           ├── nf-mashdist.{begin,err,log,out,run,sh,trace}
│       │           └── versions.yml
│       ├── meningotype
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-meningotype.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── ngmaster
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-ngmaster.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── pasty
│       │   ├── <SAMPLE_NAME>.blastn.tsv
│       │   ├── <SAMPLE_NAME>.details.tsv
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-pasty.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── pbptyper
│       │   ├── <SAMPLE_NAME>-1A.tblastn.tsv
│       │   ├── <SAMPLE_NAME>-2B.tblastn.tsv
│       │   ├── <SAMPLE_NAME>-2X.tblastn.tsv
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-pbptyper.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── seqsero2
│       │   ├── <SAMPLE_NAME>_log.txt
│       │   ├── <SAMPLE_NAME>_result.tsv
│       │   ├── <SAMPLE_NAME>_result.txt
│       │   └── logs
│       │       ├── nf-seqsero2.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── seroba
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-seroba.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── shigatyper
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-shigatyper.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── shigeifinder
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-shigeifinder.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── sistr
│       │   ├── <SAMPLE_NAME>-allele.fasta.gz
│       │   ├── <SAMPLE_NAME>-allele.json.gz
│       │   ├── <SAMPLE_NAME>-cgmlst.csv
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-sistr.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── spatyper
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-spatyper.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── ssuissero
│       │   ├── <SAMPLE_NAME>_serotyping_res.tsv
│       │   └── logs
│       │       ├── nf-ssuissero.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── staphopiasccmec
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-staphopiasccmec.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── stecfinder
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-stecfinder.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       └── tbprofiler
│           ├── <SAMPLE_NAME>.results.csv
│           ├── <SAMPLE_NAME>.results.json
│           ├── <SAMPLE_NAME>.results.txt
│           ├── bam
│           │   └── <SAMPLE_NAME>.bam
│           ├── logs
│           │   ├── nf-tbprofiler.{begin,err,log,out,run,sh,trace}
│           │   └── versions.yml
│           └── vcf
│               └── <SAMPLE_NAME>.targets.csq.vcf.gz
└── bactopia-runs
    └── merlin-<TIMESTAMP>
        ├── merged-results
        │   ├── agrvate.tsv
        │   ├── ectyper.tsv
        │   ├── emmtyper.tsv
        │   ├── genotyphi.tsv
        │   ├── hicap.tsv
        │   ├── hpsuissero.tsv
        │   ├── kleborate.tsv
        │   ├── legsta.tsv
        │   ├── logs
        │   │   └── <BACTOPIA_TOOL>-concat
        │   │       ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   ├── meningotype.tsv
        │   ├── ngmaster.tsv
        │   ├── pasty.tsv
        │   ├── pbptyper.tsv
        │   ├── seqsero2.tsv
        │   ├── seroba.tsv
        │   ├── shigatyper.tsv
        │   ├── shigeifinder.tsv
        │   ├── sistr.tsv
        │   ├── spatyper.tsv
        │   ├── ssuissero.tsv
        │   ├── staphopiasccmec.tsv
        │   └── stecfinder.tsv
        └── nf-reports
            ├── merlin-dag.dot
            ├── merlin-report.html
            ├── merlin-timeline.html
            └── merlin-trace.txt

Directory structure might be different

merlin is available as a standalone Bactopia Tool, as well as from the main Bactopia workflow (e.g. through Staphopia or Merlin). If executed from Bactopia, the merlin directory structure might be different, but the output descriptions below still apply.

Results

Merged Results

Below are results that are concatenated into a single file.

Filename	Description
agrvate.tsv	A merged TSV file with AgrVATE results from all samples
clermontyping.csv	A merged TSV file with ClermonTyping results from all samples
ectyper.tsv	A merged TSV file with ECTyper results from all samples
emmtyper.tsv	A merged TSV file with emmtyper results from all samples
genotyphi.tsv	A merged TSV file with genotyphi results from all samples
hicap.tsv	A merged TSV file with hicap results from all samples
hpsuissero.tsv	A merged TSV file with HpsuisSero results from all samples
kleborate.tsv	A merged TSV file with Kleborate results from all samples
legsta.tsv	A merged TSV file with legsta results from all samples
lissero.tsv	A merged TSV file with LisSero results from all samples
meningotype.tsv	A merged TSV file with meningotype results from all samples
ngmaster.tsv	A merged TSV file with ngmaster results from all samples
pasty.tsv	A merged TSV file with pasty results from all samples
pbptyper.tsv	A merged TSV file with pbptyper results from all samples
seqsero2.tsv	A merged TSV file with seqsero2 results from all samples
seroba.tsv	A merged TSV file with seroba results from all samples
shigapass.csv	A merged CSV file with ShigaPass results from all samples
shigatyper.tsv	A merged TSV file with ShigaTyper results from all samples
shigeifinder.tsv	A merged TSV file with ShigEiFinder results from all samples
sistr.tsv	A merged TSV file with SISTR results from all samples
spatyper.tsv	A merged TSV file with spaTyper results from all samples
ssuissero.tsv	A merged TSV file with SsuisSero results from all samples
staphopiasccmec.tsv	A merged TSV file with staphopia-sccmec results from all samples
stecfinder.tsv	A merged TSV file with stecfinder results from all samples

AgrVATE

Below is a description of the per-sample results from AgrVATE.

Extension	Description
-agr_gp.tab	A detailed report for agr kmer matches
-blastn_log.txt	Log files from programs called by AgrVATE
-summary.tab	A final summary report for agr typing

ClermonTyping

Below is a description of the per-sample results from ClermonTyping.

Extension	Description
<SAMPLE_NAME>.blast.xml	A BLAST XML file with the results of the ClermonTyping analysis
<SAMPLE_NAME>.html	A HTML file with the results of the ClermonTyping analysis
<SAMPLE_NAME>.mash.tsv	A TSV file with the Mash distances
<SAMPLE_NAME>.phylogroups.txt	A TSV file with the final phylogroup assignments

ECTyper

Below is a description of the per-sample results from ECTyper.

Filename	Description
<SAMPLE_NAME>.tsv	A tab-delimited file with ECTyper result, see ECTyper - Report format for details
blast_output_alleles.txt	Allele report generated from BLAST results

emmtyper

Below is a description of the per-sample results from emmtyper.

Filename	Description
<SAMPLE_NAME>.tsv	A tab-delimited file with emmtyper result, see emmtyper - Result format for details

hicap

Below is a description of the per-sample results from hicap.

Filename	Description
<SAMPLE_NAME>.gbk	GenBank file and cap locus annotations
<SAMPLE_NAME>.svg	Visualization of annotated cap locus
<SAMPLE_NAME>.tsv	A tab-delimited file with hicap results

HpsuisSero

Below is a description of the per-sample results from HpsuisSero.

Filename	Description
<SAMPLE_NAME>_serotyping_res.tsv	A tab-delimited file with HpsuisSero result

GenoTyphi

Below is a description of the per-sample results from GenoTyphi. A full description of the GenoTyphi output is available at GenoTyphi - Output

Filename	Description
<SAMPLE_NAME>_predictResults.tsv	A tab-delimited file with GenoTyphi results
<SAMPLE_NAME>.csv	The output of mykrobe predict in comma-separated format
<SAMPLE_NAME>.json	The output of mykrobe predict in JSON format

Kleborate

Below is a description of the per-sample results from Kleborate.

Filename	Description
<SAMPLE_NAME>.results.txt	A tab-delimited file with Kleborate result, see Kleborate - Example output for more details.

legsta

Below is a description of the per-sample results from legsta.

Filename	Description
<SAMPLE_NAME>.tsv	A tab-delimited file with legsta result, see legsta - Output for more details

LisSero

Below is a description of the per-sample results from LisSero.

Filename	Description
<SAMPLE_NAME>.tsv	A tab-delimited file with LisSero results

Mash

Below is a description of the per-sample results from Mash.

Filename	Description
<SAMPLE_NAME>-dist.txt	A tab-delimited file with mash dist results

meningotype

Below is a description of the per-sample results from meningotype .

Filename	Description
<SAMPLE_NAME>.tsv	A tab-delimited file with meningotype result

ngmaster

Below is a description of the per-sample results from ngmaster.

Filename	Description
<SAMPLE_NAME>.tsv	A tab-delimited file with ngmaster results

pasty

Below is a description of the per-sample results from pasty.

Extension	Description
.blastn.tsv	A tab-delimited file of all blast hits
.details.tsv	A tab-delimited file with details for each serogroup
.tsv	A tab-delimited file with the predicted serogroup

pbptyper

Below is a description of the per-sample results from pbptyper.

Extension	Description
.tblastn.tsv	A tab-delimited file of all blast hits
.tsv	A tab-delimited file with the predicted PBP type

SeqSero2

Below is a description of the per-sample results from SeqSero2.

Filename	Description
<SAMPLE_NAME>_result.tsv	A tab-delimited file with SeqSero2 results
<SAMPLE_NAME>_result.txt	A text file with key-value pairs of SeqSero2 results

Seroba

Below is a description of the per-sample results from Seroba. More details about the outputs are available from Seroba - Output.

Filename	Description
<SAMPLE_NAME>.tsv	A tab-delimited file with the predicted serotype
detailed_serogroup_info.txt	Detailed information about the predicted results

ShigaPass

Below is a description of the per-sample results from ShigaPass.

Extension	Description
<SAMPLE_NAME>.csv	A CSV file with the predicted Shigella or EIEC serotype

ShigaTyper

Below is a description of the per-sample results from ShigaTyyper.

Filename	Description
<SAMPLE_NAME>-hits.tsv	Detailed statistics about each individual gene hit
<SAMPLE_NAME>.tsv	The final predicted serotype by ShigaTyper

ShigEiFinder

Below is a description of the per-sample results from ShigEiFinder.

Extension	Description
<SAMPLE_NAME>.tsv	A tab-delimited file with the predicted Shigella or EIEC serotype

SISTR

Below is a description of the per-sample results from SISTR.

Filename	Description
<SAMPLE_NAME>-allele.fasta.gz	A FASTA file of the cgMLST allele search results
<SAMPLE_NAME>-allele.json.gz	JSON formated cgMLST allele search results, see SISTR - cgMLST search results for more details
<SAMPLE_NAME>-cgmlst.csv	A comma-delimited summary of the cgMLST allele search results
<SAMPLE_NAME>.tsv	A tab-delimited file with SISTR results, see SISTR - Primary results for more details

spaTyper

Below is a description of the per-sample results from spaTyper.

Filename	Description
<SAMPLE_NAME>.tsv	A tab-delimited file with spaTyper result

SsuisSero

Below is a description of the per-sample results from SsuisSero.

Filename	Description
<SAMPLE_NAME>_serotyping_res.tsv	A tab-delimited file with SsuisSero results

staphopia-sccmec

Below is a description of the per-sample results from staphopia-sccmec.

Filename	Description
<SAMPLE_NAME>.tsv	A tab-delimited file with staphopia-sccmec results

TBProfiler

Below is a description of the per-sample results from TBProfiler.

Filename	Description
<SAMPLE_NAME>.results.csv	A CSV formated TBProfiler result file of resistance and strain type
<SAMPLE_NAME>.results.json	A JSON formated TBProfiler result file of resistance and strain type
<SAMPLE_NAME>.results.txt	A text file with TBProfiler results
<SAMPLE_NAME>.bam	BAM file with alignment details
<SAMPLE_NAME>.targets.csq.vcf.gz	VCF with variant info again reference genomes

Audit Trail

Below are files that can assist you in understanding which parameters and program versions were used.

Logs

Each process that is executed will have a folder named logs. In this folder are helpful files for you to review if the need ever arises.

Extension	Description
.begin	An empty file used to designate the process started
.err	Contains STDERR outputs from the process
.log	Contains both STDERR and STDOUT outputs from the process
.out	Contains STDOUT outputs from the process
.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
.sh	The script executed by bash for the process
.trace	The Nextflow Trace report for the process
versions.yml	A YAML formatted file with program versions

Nextflow Reports

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

Filename	Description
merlin-dag.dot	The Nextflow DAG visualisation
merlin-report.html	The Nextflow Execution Report
merlin-timeline.html	The Nextflow Timeline Report
merlin-trace.txt	The Nextflow Trace report

Program Versions

At the end of each run, each of the versions.yml files are merged into the files below.

Filename	Description
software_versions.yml	A complete list of programs and versions used by each process
software_versions_mqc.yml	A complete list of programs and versions formatted for MultiQC

Parameters

Required Parameters

Define where the pipeline should find input data and save output data.

Parameter	Description
--bactopia	The path to bactopia results to use as inputs Type: string

Filtering Parameters

Use these parameters to specify which samples to include or exclude.

Parameter	Description
--include	A text file containing sample names (one per line) to include from the analysis Type: string
--exclude	A text file containing sample names (one per line) to exclude from the analysis Type: string

mashdist Parameters

Parameter	Description
--mash_sketch	The reference sequence as a Mash Sketch (.msh file) Type: string
--mash_seed	Seed to provide to the hash function Type: integer, Default: 42
--mash_table	Table output (fields will be blank if they do not meet the p-value threshold) Type: boolean
--mash_m	Minimum copies of each k-mer required to pass noise filter for reads Type: integer, Default: 1
--mash_w	Probability threshold for warning about low k-mer size. Type: number, Default: 0.01
--max_p	Maximum p-value to report. Type: number, Default: 1.0
--max_dist	Maximum distance to report. Type: number, Default: 1.0
--merlin_dist	Maximum distance to report when using Merlin . Type: number, Default: 0.1
--full_merlin	Go full Merlin and run all species-specific tools, no matter the Mash distance Type: boolean
--use_fastqs	Query with FASTQs instead of the assemblies Type: boolean

AgrVATE Parameters

Parameter	Description
--typing_only	agr typing only. Skips agr operon extraction and frameshift detection Type: boolean

ClermonTyping Parameters

Parameter	Description
--clermon_threshold	Do not use contigs under this size Type: number

ECTyper Parameters

Parameter	Description
--opid	Percent identity required for an O antigen allele match Type: integer, Default: 90
--opcov	Minumum percent coverage required for an O antigen allele match Type: integer, Default: 90
--hpid	Percent identity required for an H antigen allele match Type: integer, Default: 95
--hpcov	Minumum percent coverage required for an H antigen allele match Type: integer, Default: 50
--verify	Enable E. coli species verification Type: boolean
--print_alleles	Prints the allele sequences if enabled as the final column Type: boolean

emmtyper Parameters

Parameter	Description
--emmtyper_wf	Workflow for emmtyper to use. Type: string, Default: blast
--cluster_distance	Distance between cluster of matches to consider as different clusters Type: integer, Default: 500
--percid	Minimal percent identity of sequence Type: integer, Default: 95
--culling_limit	Total hits to return in a position Type: integer, Default: 5
--mismatch	Threshold for number of mismatch to allow in BLAST hit Type: integer, Default: 5
--align_diff	Threshold for difference between alignment length and subject length in BLAST Type: integer, Default: 5
--gap	Threshold gap to allow in BLAST hit Type: integer, Default: 2
--min_perfect	Minimum size of perfect match at 3 primer end Type: integer, Default: 15
--min_good	Minimum size where there must be 2 matches for each mismatch Type: integer, Default: 15
--max_size	Maximum size of PCR product Type: integer, Default: 2000

hicap Parameters

Parameter	Description
--database_dir	Directory containing locus database Type: string
--model_fp	Path to prodigal model Type: string
--full_sequence	Write the full input sequence out to the genbank file rather than just the region surrounding and including the locus Type: boolean
--hicap_debug	hicap will print debug messages Type: boolean
--gene_coverage	Minimum percentage coverage to consider a single gene complete Type: number, Default: 0.8
--gene_identity	Minimum percentage identity to consider a single gene complete Type: number, Default: 0.7
--broken_gene_length	Minimum length to consider a broken gene Type: integer, Default: 60
--broken_gene_identity	Minimum percentage identity to consider a broken gene Type: number, Default: 0.8

GenoTyphi Parameters

Parameter	Description
--kmer	K-mer length Type: integer, Default: 21
--min_depth	Minimum depth Type: integer, Default: 1
--model	Genotype model used. Type: string, Default: kmer_count
--report_all_calls	Report all calls Type: boolean
--mykrobe_opts	Extra Mykrobe options in quotes Type: string

Kleborate Parameters

Parameter	Description
--kleborate_preset	Preset module to use for Kleborate Type: string, Default: kpsc
--kleborate_opts	Extra options in quotes for Kleborate Type: string

legsta Parameters

Parameter	Description
--noheader	Don't print header row Type: boolean

LisSero Parameters

Parameter	Description
--min_id	Minimum percent identity to accept a match Type: number, Default: 95.0
--min_cov	Minimum coverage of the gene to accept a match Type: number, Default: 95.0

meningotype Parameters

You can use these parameters to fine-tune your meningotype analysis

Parameter	Description
--finetype	perform porA and fetA fine typing Type: boolean
--porB	perform porB sequence typing (NEIS2020) Type: boolean
--bast	perform Bexsero antigen sequence typing (BAST) Type: boolean
--mlst	perform MLST Type: boolean
--all	perform MLST, porA, fetA, porB, BAST typing Type: boolean

ngmaster Parameters

Parameter	Description
--csv	output comma-separated format (CSV) rather than tab-separated Type: boolean

pasty Parameters

Parameter	Description
--pasty_min_pident	Minimum percent identity to count a hit Type: integer, Default: 95
--pasty_min_coverage	Minimum percent coverage to count a hit Type: integer, Default: 95

pbptyper Parameters

Parameter	Description
--pbptyper_min_pident	Minimum percent identity to count a hit Type: integer, Default: 95
--pbptyper_min_coverage	Minimum percent coverage to count a hit Type: integer, Default: 95

SeqSero2 Parameters

Parameter	Description
--run_mode	Workflow to run. 'a' allele mode, or 'k' k-mer mode Type: string, Default: k
--input_type	Input format to analyze. 'assembly' or 'fastq' Type: string, Default: assembly
--bwa_mode	Algorithms for bwa mapping for allele mode Type: string, Default: mem

SISTR Parameters

Parameter	Description
--full_cgmlst	Use the full set of cgMLST alleles which can include highly similar alleles Type: boolean

spaTyper Parameters

Parameter	Description
--repeats	List of spa repeats Type: string
--repeat_order	List spa types and order of repeats Type: string
--do_enrich	Do PCR product enrichment Type: boolean

staphopia-sccmec Parameters

Parameter	Description
--hamming	Report the results as hamming distances Type: boolean

TBProfiler Profile Parameters

Parameter	Description
--call_whole_genome	Call whole genome Type: boolean
--mapper	Mapping tool to use. If you are using nanopore data it will default to minimap2 Type: string, Default: bwa
--caller	Variant calling tool to use Type: string, Default: freebayes
--calling_params	Extra variant caller options in quotes Type: string
--suspect	Use the suspect suite of tools to add ML predictions Type: boolean
--no_flagstat	Don't collect flagstats Type: boolean
--no_delly	Don't run delly Type: boolean
--tbprofiler_opts	Extra options in quotes for TBProfiler Type: string

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter	Description
--outdir	Base directory to write results to Type: string, Default: bactopia
--skip_compression	Ouput files will not be compressed Type: boolean
--datasets	The path to cache datasets to Type: string
--keep_all_files	Keeps all analysis files created Type: boolean

Max Job Request Parameters

Set the top limit for requested resources for any single job.

Parameter	Description
--max_retry	Maximum times to retry a process before allowing it to fail. Type: integer, Default: 3
--max_cpus	Maximum number of CPUs that can be requested for any single job. Type: integer, Default: 4
--max_memory	Maximum amount of memory that can be requested for any single job. Type: string, Default: 128.GB
--max_time	Maximum amount of time that can be requested for any single job. Type: string, Default: 240.h
--max_downloads	Maximum number of samples to download at a time Type: integer, Default: 3

Nextflow Configuration Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Description
--nfconfig	A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set. Type: string
--publish_dir_mode	Method used to save pipeline results to output directory. Type: string, Default: copy
--infodir	Directory to keep pipeline Nextflow logs and reports. Type: string, Default: ${params.outdir}/pipeline_info
--force	Nextflow will overwrite existing output files. Type: boolean
--cleanup_workdir	After Bactopia is successfully executed, the work directory will be deleted. Type: boolean

Institutional config options

Parameters used to describe centralized config profiles. These should not be edited.

Parameter	Description
--custom_config_version	Git commit id for Institutional configs. Type: string, Default: master
--custom_config_base	Base directory for Institutional configs. Type: string, Default: https://raw.githubusercontent.com/nf-core/configs/master
--config_profile_name	Institutional config name. Type: string
--config_profile_description	Institutional config description. Type: string
--config_profile_contact	Institutional config contact information. Type: string
--config_profile_url	Institutional config URL link. Type: string

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Description
--condadir	Directory to Nextflow should use for Conda environments Type: string
--registry	Docker registry to pull containers from. Type: string, Default: dockerhub
--datasets_cache	Directory where downloaded datasets should be stored. Type: string, Default: <BACTOPIA_DIR>/data/datasets
--singularity_cache_dir	Directory where remote Singularity images are stored. Type: string
--singularity_pull_docker_container	Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead. Type: boolean
--force_rebuild	Force overwrite of existing pre-built environments. Type: boolean
--queue	Comma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM) Type: string, Default: general,high-memory
--cluster_opts	Additional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name' Type: string
--container_opts	Additional options to pass to Apptainer, Docker, or Singularityu. (e.g. Singularity: '-D pwd' Type: string
--disable_scratch	All intermediate files created on worker nodes of will be transferred to the head node. Type: boolean

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter	Description
--monochrome_logs	Do not use coloured log outputs. Type: boolean
--nfdir	Print directory Nextflow has pulled Bactopia to Type: boolean
--sleep_time	The amount of time (seconds) Nextflow will wait after setting up datasets before execution. Type: integer, Default: 5
--validate_params	Boolean whether to validate parameters against the schema at runtime Type: boolean, Default: True
--help	Display help text. Type: boolean
--wf	Specify which workflow or Bactopia Tool to execute Type: string, Default: bactopia
--list_wfs	List the available workflows and Bactopia Tools to use with '--wf' Type: boolean
--show_hidden_params	Show all params when using --help Type: boolean
--help_all	An alias for --help --show_hidden_params Type: boolean
--version	Display version text. Type: boolean

Citations

If you use Bactopia and merlin in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• AgrVATE
  Raghuram V. AgrVATE: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants. (GitHub)

• ClermontTyping
  Beghain J, Bridier-Nahmias A, Le Nagard H, Denamur E, Clermont O. ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microbial Genomics, 4(7), e000192. (2018)

• csvtk
  Shen, W csvtk: A cross-platform, efficient and practical CSV/TSV toolkit in Golang. (GitHub)

• ECTyper
  Laing C, Bessonov K, Sung S, La Rose C ECTyper - In silico prediction of Escherichia coli serotype (GitHub)

• emmtyper
  Tan A, Seemann T, Lacey D, Davies M, Mcintyre L, Frost H, Williamson D, Gonçalves da Silva A emmtyper - emm Automatic Isolate Labeller (GitHub)

• GenoTyphi
  Wong VK, Baker S, Connor TR, Pickard D, Page AJ, Dave J, Murphy N, Holliman R, Sefton A, Millar M, Dyson ZA, Dougan G, Holt KE, & International Typhoid Consortium. An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid Nature Communications 7, 12827. (2016)

• hicap
  Watts SC, Holt KE hicap: in silico serotyping of the Haemophilus influenzae capsule locus. Journal of Clinical Microbiology JCM.00190-19 (2019)

• HpsuisSero
  Lui J HpsuisSero: Rapid Haemophilus parasuis serotyping (GitHub)

• Kleborate
  Lam MMC, Wick RR, Watts, SC, Cerdeira LT, Wyres KL, Holt KE A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat Commun 12, 4188 (2021)

• legsta
  Seemann T legsta: In silico Legionella pneumophila Sequence Based Typing (GitHub)

• LisSero
  Kwong J, Zhang J, Seeman T, Horan, K, Gonçalves da Silva A LisSero - In silico serotype prediction for Listeria monocytogenes (GitHub)

• Mash
  Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17, 132 (2016)

• meningotype
  Kwong JC, Gonçalves da Silva A, Stinear TP, Howden BP, & Seemann T meningotype: in silico typing for Neisseria meningitidis. (GitHub)

• Mykrobe
  Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook, DW, Iqbal Z Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe Wellcome Open Research 4, 191. (2019)

• ngmaster
  Kwong J, Gonçalves da Silva A, Schultz M, Seeman T ngmaster - In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST) (GitHub)

• pasty
  Petit III RA pasty: in silico serogrouping of Pseudomonas aeruginosa isolates (GitHub)

• pbptyper
  Petit III RA pbptyper: In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies (GitHub)

• SeqSero2
  Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. Appl Environ Microbiology 85(23):e01746-19 (2019)

• shigapass
  Yassine I, Hansen EE, Lefèvre S, Ruckly C, Carle I, Lejay-Collin M, Fabre L, Rafei R, Pardos de la Gandara M, Daboussi F, Shahin A, Weill FX ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies. Microb Genomics 9(3) (2023)

• ShigaTyper
  Wu Y, Lau HK, Lee T, Lau DK, Payne J In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification. Applied and Environmental Microbiology, 85(7). (2019)

• ShigEiFinder
  Zhang X, Payne M, Nguyen T, Kaur S, Lan R Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping. Microbial Genomics, 7(12). (2021)

• SISTR
  Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VPJ, Nash JHE, Taboada EN The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PloS One, 11(1), e0147101. (2016)

• spaTyper
  Sanchez-Herrero JF, and Sullivan M spaTyper: Staphylococcal protein A (spa) characterization pipeline. Zenodo. (2020)

• SsuisSero
  Lui J SsuisSero: Rapid Streptococcus suis serotyping (GitHub)

• staphopia-sccmec
  Petit III RA, Read TD Staphylococcus aureus viewed from the perspective of 40,000+ genomes. PeerJ 6, e5261 (2018)

• TBProfiler
  Phelan JE, O’Sullivan DM, Machado D, Ramos J, Oppong YEA, Campino S, O’Grady J, McNerney R, Hibberd ML, Viveiros M, Huggett JF, Clark TG Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Med 11, 41 (2019)