nextflow-strict-syntax-health/lint_results/prints-help-results/readmapping_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 26.03.1-edge

Launching `./main.nf` [adoring_woese] revision: 861ae59bc6

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

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   _____                                _______    _
  / ____|                              |__   __|  | |
 | (___   __ _ _ __   __ _  ___ _ __  ___ | | ___ | |
  \___ \ / _` | '_ \ / _` |/ _ \ '__||___|| |/ _ \| |
  ____) | (_| | | | | (_| |  __/ |        | | (_) | |____
 |_____/ \__,_|_| |_|\__, |\___|_|        |_|\___/|______|
                      __/ |
                     |___/
  sanger-tol/readmapping 1.4.0dev
------------------------------------------------------
        Typical pipeline command:

  nextflow run sanger-tol/readmapping -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.
  --outfmt                      [string]  Format for output alignment files. Accepts options: "bam" or "cram". [default: cram]
  --compression                 [string]  Output file compression type. Currently accepts: "none" or "crumble" [default: crumble]
  --merge_output                [string]  Set to a non-empty string to merge output alignment files by specimens. The string is used to name
the output directory
  --coverage_binsize            [integer] Bin size (in bp) used for computing coverage depth in the output bedGraph file. [default: 1000]

  --pacbio_adapter_fasta        [string]  Path to FASTA file contains adapter sequences for PacBio HiFi reads. [default:
${projectDir}/assets/HiFi_adapter.fasta]
  --pacbio_adapter_yaml         [string]  Path to YAML file containing guide for trimming/filtering PacBio data. See hifi-trimmer docs for
details: https://github.com/sanger-tol/hifi-trimmer [default:
${projectDir}/assets/HiFi_adapter.yaml]
  --pacbio_uli_adapter          [string]  Path to FASTA file containing the PacBio ULI adapter sequence.
  --email                       [string]  Email address for completion summary.

Reference genome options
  --fasta                       [string] Path to FASTA genome file.
  --bwamem2_index               [string] Path to directory or tar.gz archive for pre-built BWAMEM2 index.
  --header                      [string] Optional template header file for BAM/CRAM outputs

Aligner options
  --short_aligner               [string]  Alignment method to use for short-reads (options are: "minimap2" or "bwamem2"  (accepted:
minimap2, bwamem2) [default: bwamem2]
  --long_reads_map_chunk_size   [integer] Chunk size for parallel alignment of long read data, in number of sequences [default: 10000]

  --short_reads_map_chunk_size  [integer] Chunk size for parallel alignment of short read data, in number of cram containers [default:
10000]

Generic options
  --multiqc_title               [string]          MultiQC report title. Printed as page header, used for filename if not otherwise specified.
  --multiqc_logo                [string]          Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

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

* The pipeline
    https://doi.org/10.5281/zenodo.6563577

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

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