Page Comparison

module load java
nextflow run epi2me-labs/wf-alignment -profile singularity --help

N E X T F L O W  ~  version 23.12.0-edge
Launching `https://github.com/epi2me-labs/wf-alignment` [nostalgic_galileo] DSL2 - revision: e1fd7a51dc [master]
WARN: Config setting `prov.formats` is not defined, no provenance reports will be produced

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-alignment v1.1.2-ge1fd7a5
--------------------------------------------------------------------------------
Typical pipeline command:

  nextflow run epi2me-labs/wf-alignment \ 
        --fastq 'wf-alignment-demo/fastq' \ 
        --references 'wf-alignment-demo/references'

Input Options
  --fastq                [string]  FASTQ files to use in the analysis.
  --bam                  [string]  BAM or unaligned BAM (uBAM) files to use in the analysis.
  --analyse_unclassified [boolean] Analyse unclassified reads from input directory. By default the workflow will not process reads in the unclassified 
                                   directory. 
  --references           [string]  Path to a directory containing FASTA reference files.
  --reference_mmi_file   [string]  Path to an MMI index file to be used as reference.
  --counts               [string]  Path to a CSV file containing expected counts as a control.

Sample Options
  --sample_sheet         [string]  A CSV file used to map barcodes to sample aliases. The sample sheet can be provided when the input data is a directory 
                                   containing sub-directories with FASTQ files. 
  --sample               [string]  A single sample name for non-multiplexed data. Permissible if passing a single .fastq(.gz) file or directory of .fastq(.gz) 
                                   files. 

Output Options
  --out_dir              [string]  Directory for output of all workflow results. [default: output]
  --prefix               [string]  Optional prefix attached to each of the output filenames.

Advanced options
  --depth_coverage       [boolean] Calculate depth coverage statistics and include them in the report. [default: true]
  --minimap_preset       [choice]  Pre-defined parameter sets for `minimap2`, covering most common use cases. [default: dna]
                                   * dna
                                   * rna
  --minimap_args         [string]  String of command line arguments to be passed on to `minimap2`.

Miscellaneous Options
  --threads              [integer] Number of CPU threads to use for the alignment step. [default: 4]
  --disable_ping         [boolean] Enable to prevent sending a workflow ping.

Other parameters
  --monochrome_logs      [boolean] null
  --validate_params      [boolean] null [default: true]
  --show_hidden_params   [boolean] null

!! Hiding 4 params, use --show_hidden_params to show them !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-alignment for your analysis please cite:

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