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.

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

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})$

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_g360

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

Vsearch maximum sequence length.

type: integer
default: 57

Vsearch pairwise identity threshold.

type: number
default: 0.99

Parameters used for functional genomic screenings

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

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

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

sgRNA and targetting genes, tab separated

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

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

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

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

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$

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*)+$

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

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})$

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

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

Ignore JSON schema validation of the following params

hidden
type: string
default: genomes

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean