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	Required
`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`

Parameter	Description	Type	Default	Required
`aligner`	Which aligner to use	`string`	bowtie2	True
`markdup`	Which alignment postprocessor to use	`string`	bamsormadup
`run_coverage`	Run coverage analysis steps	`boolean`	True
`skip_trimming`	Skip adapter trimming	`boolean`	False
`trim_front`	Number of bases to trim from the front of the read	`integer`	0
`trim_tail`	Number of bases to trim from the tail of the read	`integer`	0
`adapter_R1`	Adapter sequence to be trimmed	`string`	None
`adapter_R2`	Adapter sequence to be trimmed	`string`	None
`disable_picard_metrics`	Disable the calculation of (slow) Picard metrics	`boolean`	False
`roi`	Region of interest for coverage analysis to be applied to all samples	`string`	None
`genelists`	Directory containing gene list bed files for granular coverage analysis	`string`	None

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

Parameter	Description	Type	Default	Hidden
`custom_config_version`	Git commit id for Institutional configs.	`string`	master	True
`custom_config_base`	Base directory for Institutional configs. Help 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.	`string`	https://raw.githubusercontent.com/nf-core/configs/master	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

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

Parameter	Description	Type	Default	Hidden
`help`	Display help text.	`boolean`		True
`version`	Display version and exit.	`boolean`		True
`publish_dir_mode`	Method used to save pipeline results to output directory. 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