strict-syntax-health/lint_results/prints-help-results/genomicrelatedness_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 26.03.0-edge

Launching `./main.nf` [agitated_bhaskara] revision: 189f7f7c11

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

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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/genomicrelatedness 1.0.0dev
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Typical pipeline command:

  nextflow run nf-core/genomicrelatedness -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.
  --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.

Reference genome options
  --fasta                            [string]  Path to FASTA reference genome file.
  --fasta_fai                        [string]  Path to FASTA index (.fai) file for the reference genome.
  --dict                             [string]  Path to sequence dictionary (.dict) for the reference genome.
  --bwamem2_index                    [string]  Path to directory containing the BWA-MEM2 index for the reference genome.
  --intervals                        [string]  Path to directory containing the intervals in bed format.
  --target_number_of_interval_files  [integer] Number of interval files to split the reference genome into for parallel processing.
  --max_number_of_intervals_per_file [integer] Maximum number of intervals per interval file for parallel processing.

Variant set options
  --known_variants_vcf               [string, null]        Path to known variant set vcf file.
  --known_variants_tbi               [string, null]        Path to known variant set tabix index tbi file.
  --bootstrapping_rounds             [integer, null]       Number of bootstrapping rounds to perform when generating a variant set.
  --include_scaffolds                [string, array, null] List of scaffolds (e.g., chromosome or contig names) to include using vcftools. Can be passed as
single string, array of strings, path to text file (including .bed). Leave empty to choose all by
default.
  --exclude_scaffolds                [string, array, null] List of scaffolds (e.g., chromosome or contig names) to exclude using vcftools. Can be passed as
single string, array of strings, path to text file (including .bed). Leave empty to disable
exclusion.

Stages options
  --hard_filter_variants             [boolean] Whether to perform hard filtering of variants.
  --skip_bqsr                        [boolean] Whether to skip Base Quality Score Recalibration (BQSR) on the aligned reads.
  --skip_variant_calling             [boolean] Whether to skip the variant calling stage to identify variants from the aligned reads.
  --skip_intersection_thinning       [boolean] Whether to skip the intersection and thinning of the called variants to a set of high-quality,
independent variants for relatedness estimation.
  --skip_relatedness_estimation      [boolean] Whether to skip the relatedness estimation stage.

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

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