Skip to content

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 \ 
  --include includes.txt  

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

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

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

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
--skip_resistance Turn off resistance genes screening
Type: boolean
--skip_kaptive Turn off Kaptive screening of K and O loci
Type: boolean
--min_identity Minimum alignment percent identity for main results
Type: number, Default: 90.0
--kleborate_min_coverage Minimum alignment percent coverage for main results
Type: number, Default: 80.0
--min_spurious_identity Minimum alignment percent identity for spurious results
Type: number, Default: 80.0
--min_spurious_coverage Minimum alignment percent coverage for spurious results
Type: number, Default: 40.0
--min_kaptive_confidence Minimum Kaptive confidence to call K/O loci - confidence levels below this will be reported as unknown
Type: string, Default: Good
--force_index Rebuild the BLAST index at the start of execution
Type: boolean

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
--pbptyper_min_ani Minimum S. pneumoniae ANI to predict PBP Type
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

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 (in GB) that can be requested for any single job.
Type: integer, Default: 32
--max_time Maximum amount of time (in minutes) that can be requested for any single job.
Type: integer, Default: 120
--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.