Skip to content

Latest commit

 

History

History
130 lines (90 loc) · 9.58 KB

parameters.md

File metadata and controls

130 lines (90 loc) · 9.58 KB

avantonder/assembleBAC-ONT pipeline parameters

This pipeline assembles ONT sequence 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 file containing information about the samples in the experiment.
HelpYou 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. See usage docs.
 string True
fastq_dir Path to a folder containing fastq files from the Nanopore run. 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.
HelpSet 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

filtlong

Parameters used when running filtlong

Parameter Description Type Default Required Hidden
min_read_length Minimum read length to keep integer 6000

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 string 4.3mb

medaka

Parameters used when running Medaka

Parameter Description Type Default Required Hidden
medaka_model Medaka model to use string None

flye

Parameters used when running flye

Parameter Description Type Default Required Hidden
flye_mode Data type (options are: --nano-raw,--nano-corr,--nano-hq ) string --nano-hq

mlst

Parameters used when running mlst

Parameter Description Type Default Required Hidden
skip_mlst Skip MLST with mlst boolean

Assembly QC options

Parameter Description Type Default Required Hidden
skip_assemblyqc Skip assembly QC with CheckM2 and Quast boolean
checkm2db Path to CheckM2 DIAMOND database file string

Annotation options

Parameter Description Type Default Required Hidden
skip_annotation Skip annotation with Bakta boolean
baktadb Path to Bakta database directory string
proteins Fasta file of trusted protein sequences for CDS annotation string None
prodigal_tf Path to existing Prodigal training file to use for CDS prediction string None

Reference genome options

Reference genome related files and options required for the workflow.

Parameter Description Type Default Required Hidden
fasta Path to FASTA genome file.
HelpThis parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
 string True

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.
HelpIf 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.
HelpUse 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.
HelpUse 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.
HelpUse 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
version Display version and exit. boolean True
publish_dir_mode Method used to save pipeline results to output directory.
HelpThe 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.
HelpAn 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
HelpIncoming 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
validationShowHiddenParams Show all params when using --help
HelpBy 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
validationFailUnrecognisedParams Validation of parameters fails when an unrecognised parameter is found.
HelpBy default, when an unrecognised parameter is found, it returns a warinig.
 boolean True
validationLenientMode Validation of parameters in lenient more.
HelpAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
 boolean True