Pipeline Parameters

Documentation for all available parameters, generated automatically from nextflow_schema.json.

Input/output options

Define where the pipeline should find input data and save output data.

Parameter	Default	Description
--input string required	-	Path to comma-separated file containing information about the samples in the experiment. file-path More info You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.
--outdir string required	-	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. directory-path
--email string	-	Email address for completion summary. More info Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.
--multiqc_title string	-	MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Reference genome options

Reference genome related files and options required for the workflow.

Parameter	Default	Description
--genome string	-	Name of iGenomes reference. Options: GRCh38 CHM13 More info If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. See the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.
--vep_cache string	-	Path to VEP cache directory. More info Path to the directory containing the VEP cache. If you are using an iGenomes reference, this will be set automatically. Otherwise, you will need to provide this path yourself.
--vep_cache_version integer	-	Version of the VEP cache to use. More info The version of the VEP cache to use. This should match the version of VEP being used.
--vep_args string	-	Additional command line arguments to pass to VEP.

minimap2 options

Parameter	Default	Description
--minimap2_ont_model string	-	Minimap ont model to use
--minimap2_pb_model string	-	Minimap Pacbio model to use
--save_secondary_alignment boolean	true	Whether to save secondary alignments

ASCAT parameters

ASCAT specific parameters

Parameter	Default	Description
--ascat_ploidy string	-	Enforce a ploidy
--ascat_purity string	-	Enforce a purity
--ascat_penalty integer	150	Penalty value
--ascat_min_base_qual integer	20	Minimum base quality for allelecounter
--ascat_min_counts integer	10	Minimum counts for allelecounter
--ascat_min_map_qual integer	10	Minimum mapping quality for allelecounter
--ascat_longread_bins integer	2000	Binsize for long-read
--ascat_allelecounter_flags string	-f 0	Additional allelecounter flags to use
--ascat_chroms string	-	Chromosomes to process (automatically inferred, only use if you want to run on a subset)
--ascat_gc_files string	-	Path to (zip) of GC files
--ascat_rt_files string	-	path to (zip) of RT files
--ascat_pdf_plots boolean	-	Boolean for ASCAT production of pdf plots (entered as string)

Skip options

Define whether to skip certain steps

Parameter	Default	Description
--skip_qc boolean	-	Skips all QC steps
--skip_cramino boolean	-	Skips Cramino
--skip_mosdepth boolean	-	Skips Mosdepth
--skip_bamstats boolean	-	Skips samtools flagstat, stats, and idxstats
--skip_wakhan boolean	-	Skips wakhan
--skip_fiber boolean	-	Skip Fibertools steps
--skip_ascat boolean	-	Skip ASCAT
--skip_m6a boolean	-	Skip m6a calling by Fibertools

Generic options

Less common options for the pipeline, typically set in a config file.

Parameter	Default	Description
--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).

Hidden / Advanced Parameters

Reference genome options

Reference genome related files and options required for the workflow.

Parameter	Default	Description
--igenomes_ignore boolean	-	Do not load the iGenomes reference config. More info Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.
--igenomes_base string	s3://ngi-igenomes/igenomes/	The base path to the igenomes reference files directory-path

Institutional config options

Parameters used to describe centralised config profiles. These should not be edited.

Parameter	Default	Description
--custom_config_version string	master	Git commit id for Institutional configs.
--custom_config_base string	https://raw.githubusercontent.com/nf-core/configs/master	Base directory for Institutional configs. More info If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
--config_profile_name string	-	Institutional config name.
--config_profile_description string	-	Institutional config description.
--config_profile_contact string	-	Institutional config contact information.
--config_profile_url string	-	Institutional config URL link.

Generic options

Less common options for the pipeline, typically set in a config file.

Parameter	Default	Description
--version boolean	-	Display version and exit.
--publish_dir_mode string	copy	Method used to save pipeline results to output directory. Options: symlink rellink link copy copyNoFollow move More info The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.
--email_on_fail string	-	Email address for completion summary, only when pipeline fails. More info An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
--plaintext_email boolean	-	Send plain-text email instead of HTML.
--max_multiqc_email_size string	25.MB	File size limit when attaching MultiQC reports to summary emails.
--monochrome_logs boolean	-	Do not use coloured log outputs.
--hook_url string	-	Incoming hook URL for messaging service More info Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
--multiqc_config string	-	Custom config file to supply to MultiQC. file-path
--multiqc_logo string	-	Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
--validate_params boolean	true	Boolean whether to validate parameters against the schema at runtime
--pipelines_testdata_base_path string	https://raw.githubusercontent.com/nf-core/test-datasets/	Base URL or local path to location of pipeline test dataset files
--trace_report_suffix string	-	Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
--normal_fiber boolean	true	do fiber-seq on normal samples