parameters.md

nf-cmgg/preprocessing pipeline parameters

Demultiplexing, adapter trimming, alignment, and coverage calculation for NGS data.

Input/output options

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

Parameter	Description	Type	Default	Required	Hidden
input	Path to comma-separated or yaml file containing information about the samples in the experiment. Help 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.	string		True
outdir	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.	string		True
email	Email address for completion summary. Help 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	MultiQC report title. Printed as page header, used for filename if not otherwise specified.	string
genomes		object			True

Pipeline options

Parameter	Description	Type	Default	Required	Hidden
split_fastq	Specify how many reads each split of a FastQ file contains. Set 0 to turn off splitting at all. Help Use the tool FastP to split FASTQ file by number of reads. This parallelizes across fastq file shards speeding up mapping. Note although the minimum value is 250 reads, if you have fewer than 250 reads a single FASTQ shard will still be created.	integer	100000000
genelists	Directory containing gene list bed files for granular coverage analysis	string	None

Institutional config options

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

Parameter	Description	Type	Default	Required	Hidden
custom_config_version	Git commit id for Institutional configs.	string	main		True
custom_config_base	Base directory for custom configs. Help If you're running offline, Nextflow will not be able to fetch the custom 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.	string	https://raw.githubusercontent.com/nf-cmgg/configs/main		True
config_profile_name	Institutional config name.	string			True
config_profile_description	Institutional config description.	string			True
config_profile_contact	Institutional config contact information.	string			True
config_profile_url	Institutional config URL link.	string			True

Generic options

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

Parameter	Description	Type	Default	Required	Hidden
version	Display version and exit.	boolean			True
publish_dir_mode	Method used to save pipeline results to output directory. (accepted: symlink|rellink|link|copy|copyNoFollow|move) Help 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 for details.	string	copy		True
email_on_fail	Email address for completion summary, only when pipeline fails. Help An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.	string			True
plaintext_email	Send plain-text email instead of HTML.	boolean			True
max_multiqc_email_size	File size limit when attaching MultiQC reports to summary emails.	string	25.MB		True
monochrome_logs	Do not use coloured log outputs.	boolean			True
hook_url	Incoming hook URL for messaging service Help Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.	string			True
multiqc_config	Custom config file to supply to MultiQC.	string			True
multiqc_logo	Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file	string			True
multiqc_methods_description	Custom MultiQC yaml file containing HTML including a methods description.	string
validate_params	Boolean whether to validate parameters against the schema at runtime	boolean	True		True
pipelines_testdata_base_path	Base URL or local path to location of pipeline test dataset files	string	https://raw.githubusercontent.com/nf-core/test-datasets/		True
trace_report_suffix	Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.	string			True
help	Display the help message.	['boolean', 'string']
help_full	Display the full detailed help message.	boolean
show_hidden	Display hidden parameters in the help message (only works when --help or --help_full are provided).	boolean
igenomes_base	Directory / URL base for iGenomes references.	string	/references/		True
igenomes_ignore	Do not load the iGenomes reference config. Help 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.	boolean			True
genome	Name of iGenomes reference. Help 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 for more details.	string