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

Path to comma-separated file containing information about the samples in the experiment.

type: string
pattern: ^\S+\.csv$

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. See usage docs.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Type of analysis to perform. Targeted for targeted CRISPR experiments and screening for CRISPR screening experiments.

required
type: string

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

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 report title. Printed as page header, used for filename if not otherwise specified.

type: string

Alternative pipeline steps to include in the targeted analysis.

Trim overrepresented sequences from reads (cutadapt)

type: boolean

If the sample contains umi-molecular identifyers (UMIs), run the UMI extraction, clustering and consensus steps.

type: boolean

Parameters regarding umi molecular identifiers (UMIs)

Minimum size of a UMI cluster.

type: integer
default: 1

Medaka model (-m) to use according to the basecaller used.

type: string
default: r941_min_high_g303

Parameters used for alignment processes

Aligner program to use.

type: string

Provide the same protospacer sequence for all samples. Will override protospacer sequences provided by an input samplesheet.

type: string

Parameters to use in Vsearch processes

Vsearch minimum sequence length.

type: integer
default: 55

Discard sequences shorter than vsearch_minseqlength.

Vsearch maximum sequence length.

type: integer
default: 57

Discard sequences longer than vsearch_minseqlength.

Vsearch pairwise identity threshold.

type: number
default: 0.99

Do not add the target to the cluster if the pairwise identity with the centroid is lower than id. The pairwise identity is defined as the number of (matching columns) / (alignment length - terminal gaps).

Parameters used for functional genomic screenings

sgRNA and targetting genes, tab separated

type: string
pattern: ^\S+\.(tsv|txt)$

Sequencing adapter sequence to use for trimming on the 5' end

type: string

Sequencing adapter sequence to use for trimming on the 3' end

type: string

Fasta file in case you want to map with bowtie2 and then MAGeCK count

type: string

Design matrix used for MAGeCK MLE to call essential genes under multiple conditions while considering sgRNA knockout efficiency

type: string

Comma-separated file with the conditions to be compared. The first one will be the reference (control)

type: string

Parameter indicating if MAGeCK RRA should be ran instead of MAGeCK MLE.

type: boolean

Please provide your count table if the mageck test should be skipped.

type: string
pattern: ^\S+\.(tsv|txt)$

sgRNA library annotation for crisprcleanR

type: string

a filter threshold value for sgRNAs, based on their average counts in the control sample

type: number
default: 30

Minimal number of different genes targeted by sgRNAs in a biased segment in order for the corresponding counts to be corrected for CRISPRcleanR

type: number
default: 3

Core essential gene set for BAGEL2

type: string
default: https://raw.githubusercontent.com/hart-lab/bagel/master/CEGv2.txt

Non essential gene set for BAGEL2

type: string
default: https://raw.githubusercontent.com/hart-lab/bagel/master/NEGv1.txt

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

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.

Path to the reference FASTA file. Will override reference sequences provided by an input sample sheet.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

Do not load the iGenomes reference config.

hidden
type: boolean

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.

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

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

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.

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

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

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

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'

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

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'

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

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

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.

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

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.

Ignore JSON schema validation of the following params

hidden
type: string
default: genomes,igenomes_base

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

By default, when an unrecognised parameter is found, it returns a warinig.

Validation of parameters in lenient more.

hidden
type: boolean

Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.