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$

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

Skip the classification of samples by clonality.

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: https://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g303_model.hdf5

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
pattern: ^[ACGTacgt]+$

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

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

Library in fasta file format in case you want to map with bowtie2 and then MAGeCK count

type: string

Specify the label for control sample (usually day 0 or plasmid). For every other sample label, the module will treat it as a treatment condition and compare with control sample for MAGeCK MLE

type: string

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

type: string

control-sgrna file for MAGeCK MLE

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 MLE should be run

type: boolean

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

type: boolean

Parameter indicating if BAGEL2 should be run

type: boolean

Parameter indicating if DrugZ should be run

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

Essential genes to remove from the drugZ modules

type: string
pattern: \\S+

Specify to run the Hitselection algorithm

type: boolean

Number of iterations the hit selection module should provide

type: number
default: 1000

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

The base path to the igenomes reference files

hidden
type: string
default: s3://ngi-igenomes/igenomes/

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

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

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

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/