parameters.md

avantonder/bovisanalyzer pipeline parameters

nextflow pipeline for analyzing Mycobacterium bovis genomes

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 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. It has to be a comma-separated file with 3 columns, and a header row.	string
reference	Path to reference genome	string	None
kraken2db	Path to Kraken 2 database	string	None
outdir	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.	string
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.	string
multiqc_title	MultiQC report title. Printed as page header, used for filename if not otherwise specified.	string

Quality Control options

Parameter	Description	Type	Default	Required	Hidden
skip_fastp	Skip the fastp trimming step.	boolean
skip_fastqc	Skip the fastQC step.	boolean
save_trimmed_fail	Save failed trimmed reads.	boolean
skip_multiqc	Skip MultiQC.	boolean
adapter_file	Path to file containing adapters in FASTA format.	string	'${baseDir}/assets/adapters.fas'
skip_kraken2	Skip Kraken 2 and Bracken.	boolean

Sub-sampling options

Parameter	Description	Type	Default	Required	Hidden
skip_subsampling	Skip sub-sampling with Rasusa.	boolean
subsampling_depth_cutoff	Desired coverage depth when sub-sampling.	integer	100
genome_size	Genome size for sub-sampling (set to 4.3 Mb for M. bovis).	string	4.3mb

Clustering options

Parameter	Description	Type	Default	Required	Hidden
skip_clusters	Skip APHA clustering	boolean

Alignment options

Parameter	Description	Type	Default	Required	Hidden
non_GATC_threshold	Maximum non GATC bases (i.e - and N) to allow in pseudogenome sequences.	number	0.25
skip_alignment	Skip alignment step.	boolean

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	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

Max job request options

Set the top limit for requested resources for any single job.

Parameter	Description	Type	Default	Required	Hidden
max_cpus	Maximum number of CPUs that can be requested for any single job. Help Use to set an upper-limit for the CPU requirement for each process. Should be an
integer e.g. --max_cpus 1	integer	16		True
max_memory	Maximum amount of memory that can be requested for any single job. Help Use to set an upper-limit for the memory requirement for each process. Should
be a string in the format integer-unit e.g. --max_memory '8.GB'	string	128.GB		True
max_time	Maximum amount of time that can be requested for any single job. Help Use to set an upper-limit for the time requirement for each process. Should be a
string in the format integer-unit e.g. --max_time '2.h'	string	240.h		True

Generic options

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

Parameter	Description	Type	Default	Required	Hidden
help	Display help text.	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
multiqc_config	Custom config file to supply to MultiQC.	string			True
tracedir	Directory to keep pipeline Nextflow logs and reports.	string	${params.outdir}/pipeline_info		True
validate_params	Boolean whether to validate parameters against the schema at runtime	boolean	True		True
show_hidden_params	Show all params when using --help Help By default, parameters set as hidden in the schema are not shown on the command line when a user
runs with --help. Specifying this option will tell the pipeline to show all parameters.	boolean			True
enable_conda	Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.	boolean			True