strict-syntax-health/lint_results/prints-help-results/seqinspector_help.txt at main · nf-core/strict-syntax-health · GitHub

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$ NXF_SYNTAX_PARSER=v2 nextflow run . --help


 N E X T F L O W   ~  version 26.02.0-edge

Downloading plugin nf-core-utils@0.4.0
Downloading plugin nf-schema@2.6.1
Launching `./main.nf` [chaotic_austin] revision: e9312db940


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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/seqinspector 1.1.0dev
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Typical pipeline command:

  nextflow run nf-core/seqinspector -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.
  --sample_size                      [number] Take a subset of reads for analysis. [default: 0]
  --outdir                           [string] The output directory where the results will be saved. You have to use absolute paths to storage on
Cloud infrastructure.
  --email                            [string] Email address for completion summary.
  --multiqc_title                    [string] MultiQC report title. Printed as page header, used for filename if not otherwise specified.
  --tools                            [string] Comma-separated string of tools to run
  --tools_bundle                     [string] Select some default setup for the tools to be run, tools can still be used to add tools
[default: default]
  --skip_tools                       [string] Comma-separated string of tools to skip - overrides any other means of tools selection

Validation options
  --fq_lint_args                     [string]  Arguments to pass to FQ lint
  --continue_with_lint_fail          [boolean] Whether to continue with the pipeline if linting fails for a single sample. [default: true]
  --checkqc_config                   [string]  Path to custom CheckQC config

Kraken2 options
  --kraken2_db                       [string]  Path to Kraken2 database file, either a gzipped file or the path to the uncompressed database.

  --kraken2_save_reads               [boolean] Turn on saving of Kraken2-aligned reads
  --kraken2_save_readclassifications [boolean] Turn on saving of Kraken2 per-read taxonomic assignment file
  --kraken_save_uncompressed_db      [boolean] Turn on saving of uncompressed Kraken2 DB

Reference genome options
  --genome                           [string] Name of iGenomes reference.
  --fastq_screen_references          [string] A .csv of reference genomes to be mapped against by FastQ Screen [default:
${projectDir}/assets/example_fastq_screen_references.csv]
  --fasta                            [string] Path to FASTA genome file.
  --bwamem2                          [string] Path to bwamem2 indices.
  --dict                             [string] Sequence dictionary for the reference fasta file provided.
  --fai                              [string] Fasta index for the reference fasta file provided.
  --target_intervals                 [string] Path to target intervals file.
  --bait_intervals                   [string] Path to bait intervals file.

Generic options
  --multiqc_methods_description      [string]          Custom MultiQC yaml file containing HTML including a methods description.
  --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 20 param(s), use the `--showHidden` parameter to show them !!
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* The pipeline
    https://doi.org/10.5281/zenodo.18757486

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

* Software dependencies
    https://github.com/nf-core/seqinspector/blob/master/CITATIONS.md