strict-syntax-health/lint_results/prints-help-results/bamtofastq_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 26.04.3

Downloading plugin nf-schema@2.6.1
Launching `./main.nf` [condescending_stonebraker] revision: 1a4d4b58aa


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  |\ | |__  __ /  ` /  \ |__) |__         }  {
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                                        `._,._,'
  nf-core/bamtofastq 2.3.0dev
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Typical pipeline command:

  nextflow run nf-core/bamtofastq -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.

Main options
  --chr                         [string]  Only use reads mapping to a specific chromosome/region. Has to be specified as in bam: i.e chr1,
chr{1..22} (gets all reads mapping to chr1 to 22), 1, "X Y", incorrect naming will lead to a
potentially silent error.
  --no_read_QC                  [boolean] If specified, no quality control will be performed on extracted reads. Useful, if this is done
anyways in the subsequent workflow.
  --no_stats                    [boolean] If specified, skips all quality control and stats computation, including `FastQC` on both input bam
and output reads, `samtools flagstat`, `samtools idxstats`, and `samtools stats`.
  --reads_in_memory             [integer] Reads to store in memory [default = '100000']. Only relevant for use with `--samtools_collate_fast`.
[default: 100000]
  --samtools_collate_fast       [boolean] Uses fast mode for samtools collate in `sortExtractMapped`, `sortExtractUnmapped` and
`sortExtractSingleEnd`.

Reference genome options
  --genome                      [string] Name of iGenomes reference.
  --fasta                       [string] Path to FASTA genome file.
  --fasta_fai                   [string] Path to FASTA FAI genome index file.

Generic options
  --email                       [string]          Email address for completion summary.
  --multiqc_title               [string]          MultiQC report title. Printed as page header, used for filename if not otherwise specified.
  --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 19 param(s), use the `--showHidden` parameter to show them !!
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* The pipeline
    https://doi.org/10.5281/zenodo.4710628

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

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