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bash
source /local/cluster/bactopia/activate.sh

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$ echo $BACTOPIADB
/nfs1/CGRB/databases/bactopia/latest

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bactopia datasets

# Paired-end
bactopia --R1 R1.fastq.gz --R2 R2.fastq.gz --sample SAMPLE_NAME \
         --datasets datasets/ --outdir OUTDIR

# Single-End
bactopia --SE SAMPLE.fastq.gz --sample SAMPLE --datasets datasets/ --outdir OUTDIR

# Multiple Samples
bactopia prepare MY-FASTQS/ > fastqs.txt
bactopia --fastqs fastqs.txt --datasets datasets --outdir OUTDIR

# Single ENA/SRA Experiment
bactopia --accession SRX000000 --datasets datasets --outdir OUTDIR

# Multiple ENA/SRA Experiments
bactopia search "staphylococcus aureus" > accessions.txt
bactopia --accessions accessions.txt --dataset datasets --outdir ${OUTDIR}

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$ which bactopia
/local/cluster/bactopia/bin/bactopia
$ bactopia --version
bactopia 2.1.0

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$ bactopia --help
N E X T F L O W  ~  version 22.04.0
Launching `/local/cluster/bactopia/share/bactopia-2.1.x/main.nf` [backstabbing_visvesvaraya] DSL2 - revision: bd75c553f9


---------------------------------------------
   _                _              _
  | |__   __ _  ___| |_ ___  _ __ (_) __ _
  | '_ \ / _` |/ __| __/ _ \| '_ \| |/ _` |
  | |_) | (_| | (__| || (_) | |_) | | (_| |
  |_.__/ \__,_|\___|\__\___/| .__/|_|\__,_|
                            |_|
  bactopia v2.1.0
  Bactopia is a flexible pipeline for complete analysis of bacterial genomes.
---------------------------------------------
Typical pipeline command:

  bactopia --fastqs samples.txt --datasets datasets/ --species 'Staphylococcus aureus' -profile singularity

Required Parameters
  ### For Procesessing Multiple Samples
  --samples                           [string]  A FOFN (via bactopia prepare) with sample names and paths to FASTQ/FASTAs to process

  ### For Processing A Single Sample
  --R1                                [string]  First set of compressed (gzip) paired-end FASTQ reads (requires --R2 and --sample)
  --R2                                [string]  Second set of compressed (gzip) paired-end FASTQ reads (requires --R1 and --sample)
  --SE                                [string]  Compressed (gzip) single-end FASTQ reads  (requires --sample)
  --ont                               [boolean] Treat `--SE` or `--accession` as long reads for analysis. (requires --sample if using --SE)
  --hybrid                            [boolean] Treat `--SE` as long reads for hybrid assembly.  (requires --R1, --R2, --SE and --sample)
  --short_polish                      [boolean] Treat `--SE` as long reads for long-read assembly and short read polishing.  (requires --R1, --R2, --SE and
                                                --sample)
  --sample                            [string]  Sample name to use for the input sequences

  ### For Downloading from SRA/ENA or NCBI Assembly
  **Note: Downloaded assemblies will have error free Illumina reads simulated for processing.**
  --accessions                        [string]  A file containing ENA/SRA Experiment accessions or NCBI Assembly accessions to processed
  --accession                         [string]  Sample name to use for the input sequences

  ### For Processing an Assembly
  **Note: Assemblies will have error free Illumina reads simulated for processing.**
  --assembly                          [string]  A assembled genome in compressed FASTA format. (requires --sample)
  --check_samples                     [boolean] Validate the input FOFN provided by --samples

Dataset Parameters
  --datasets                          [string]  The path to datasets that have already been set up
  --species                           [string]  Name of species for species-specific dataset to use
  --ask_merlin                        [boolean] Ask Merlin to execute species specific Bactopia tools based on Mash distances
  --coverage                          [integer] Reduce samples to a given coverage [default: 100]
  --genome_size                       [string]  Expected genome size (bp) for all samples, a value of '0' will disable read error correction and read
                                                subsampling, otherwise estimate with Mash [default: 0]

Annotate Genome Parameters
  --use_bakta                         [boolean] Use Bakta for genome annotation (requires --bakta_db)

Optional Parameters
  --outdir                            [string]  Base directory to write results to [default: ./]
  --run_name                          [string]  Name of the directory to hold results [default: bactopia]

Helpful Parameters
  --wf                                [string]  Specify which workflow or Bactopia Tool to execute [default: bactopia]
  --list_wfs                          [boolean] List the available workflows and Bactopia Tools to use with '--wf'
  --help_all                          [boolean] An alias for --help --show_hidden_params
  --version                           [boolean] Display version text.

!! Hiding 149 params, use --show_hidden_params (or --help_all) to show them !!
--------------------------------------------------------------------
If you use bactopia for your analysis please cite:

* Bactopia
  https://doi.org/10.1128/mSystems.00190-20

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://bactopia.github.io/acknowledgements/
--------------------------------------------------------------------