nextflow-strict-syntax-health/lint_results/prints-help-results/curationpretext_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

Launching `./main.nf` [special_stallman] revision: 138610ecf1

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

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  \___ \ / _` | '_ \ / _` |/ _ \ '__||___|| |/ _ \| |
  ____) | (_| | | | | (_| |  __/ |        | | (_) | |____
 |_____/ \__,_|_| |_|\__, |\___|_|        |_|\___/|______|
                      __/ |
                     |___/
  sanger-tol/curationpretext 1.6.1
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        Typical pipeline command:

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

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

Input/output options
  --input           [string]  Input fasta file
  --split_telomere  [boolean] Split the telomere file into 5' and 3' files for seperate ingestion into the HiC maps [default:
false]
  --skip_tracks     [string]  Skip generation for specified tracks
  --reads           [array]   Input longread fasta files
  --read_type       [string]  Type of longread data  (accepted: hifi, clr, ont, illumina)
  --cram            [array]   Input cram files
  --teloseq         [string]  Telomeric Motif for search. Defaults to TTAGGG
  --map_order       [string]  HiC map scaffold order. Default to unsorted  (accepted: length, unsorted)
  --aligner         [string]  Aligner for use {minimap2, bwamem2} in generating map  (accepted: bwamem2, minimap2, AUTO)
  --run_hires       [boolean] Run High Resolution pretext maps
  --run_ultra       [string]  Run Ultra resolution pretext maps  (accepted: yes, no, force)
  --cram_chunk_size [integer] Chunk size for splitting CRAM files [default: 10000]
  --pre_mapped_bam  [string]  Pre-mapped BAM file
  --snapshot_order  [string]  Order of scaffolds in the png
  --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.
  --sample          [string]  A Name for the sample
  --all_output      [boolean] Output all files [default: false]
  --multi_mapping   [number]  MAPQ values used to filter reads. [default: 0]

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 16 param(s), use the `--showHidden` parameter to show them !!
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* The pipeline
    https://doi.org/10.5281/zenodo.12773958

* The nf-core framework
    https://doi.org/10.5281/zenodo.12773958

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