nextflow-strict-syntax-health/lint_results/prints-help-results/blobtoolkit_help.txt at main · sanger-tol/nextflow-strict-syntax-health · GitHub

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$ NXF_SYNTAX_PARSER=v2 nextflow run . --help


 N E X T F L O W   ~  version 26.03.0-edge

Downloading plugin nf-schema@2.5.1
Launching `./main.nf` [zen_bose] revision: 85ba1c7951

WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'

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  \___ \ / _` | '_ \ / _` |/ _ \ '__||___|| |/ _ \| |
  ____) | (_| | | | | (_| |  __/ |        | | (_) | |____
 |_____/ \__,_|_| |_|\__, |\___|_|        |_|\___/|______|
                      __/ |
                     |___/
  sanger-tol/blobtoolkit 0.10.0
------------------------------------------------------
        Typical pipeline command:

  nextflow run sanger-tol/blobtoolkit -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>

help message of that parameter will be printed.
or `--helpFull`.

Input/output options
  --input                [string]  Path to comma-separated file containing information about the samples in the experiment.
  --align                [boolean] Turn on optional alignment before running the rest of the pipeline.
  --mask                 [boolean] Turn on optional genome masking if needed.
  --skip_taxon_filtering [boolean] Skip filtering out hits from the same species in blast* searches.
  --fetchngs_samplesheet [boolean] Turn on the conversion from a nf-core/fetchngs samplesheet.
  --busco_lineages       [string]  Name of the ODB lineages to run BUSCO on. By default, the pipeline will automatically select the
correct lineage based on the taxonomy. The three basal lineages `eukaryota`, `bacteria`, and
`archaea`, do *not* need to be listed as they are _always_ included.
  --busco_gene_predictor [string]  Name of the gene predictor to run BUSCO on. By default, the pipeline will automatically select
miniprot for gene prediction.  (accepted: miniprot, metaeuk, augustus)
  --precomputed_busco    [string]  Directory containing precomputed BUSCO results (each named as `run_{lineage}_odbxx`), which can be
supplied to skip running BUSCO in the pipeline.
  --image_format         [string]  Select the format of the output images.  (accepted: png, svg) [default: png]
  --blast_annotations    [string]  Control whether to use all, `blastp` (for minimal annotations), `blastx` (for both blastp and blastx
annotations) or `no` blast annotations.  (accepted: all, blastp, blastx, off) [default: all]

  --outdir               [string]  The output directory where the results will be saved. You have to use absolute paths to storage on
Cloud infrastructure. [default: results]
  --email                [string]  Email address for completion summary.
  --multiqc_title        [string]  MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Reference genome options
  --taxon                [string, integer] Name or taxonomy ID for the genome species
  --accession            [string]          Genome accession where available or an identifier for draft assemblies
  --fasta                [string]          Path to FASTA genome file.

Databases
  --busco                [string] Local directory where clade-specific BUSCO lineage datasets are stored
  --lineage_tax_ids      [string] File that holds a mapping between BUSCO lineages and taxon IDs.
  --blastp               [string] Path to the Diamond species-specific buscogenes database
  --blastx               [string] Path to the Diamond species-specific buscoregions database
  --blastn               [string] Path to the nucleotide BLAST database
  --taxdump              [string] Path to the new NCBI tax dump database

Execution
  --use_work_dir_as_temp [boolean] Set to true to make tools (e.g. sort, FastK, MerquryFK, BLASTP, BLASTX) use the work directory for
their temporary files, rather than the system default.

Generic options
  --help                 [boolean, string] Display the help message.
  --help_full            [boolean]         Display the full detailed help message.
  --show_hidden          [boolean]         Display hidden parameters in the help message (only works when --help or --help_full are provided).

 !! Hiding 18 param(s), use the `--showHidden` parameter to show them !!
------------------------------------------------------

* The pipeline
    https://doi.org/10.5281/zenodo.7949058

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

* Software dependencies
    https://github.com/sanger-tol/blobtoolkit/blob/main/CITATIONS.md