nf-core/crisprseq
A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (targeted
) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (screening
).
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.
string
^\S+\.csv$
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Type of analysis to perform. Targeted for targeted CRISPR experiments and screening for CRISPR screening experiments.
string
Email address for completion summary.
string
^([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.
string
Alternative pipeline steps to include in the targeted analysis.
Trim overrepresented sequences from reads (cutadapt)
boolean
If the sample contains umi-molecular identifyers (UMIs), run the UMI extraction, clustering and consensus steps.
boolean
Skip the classification of samples by clonality.
boolean
Parameters regarding umi molecular identifiers (UMIs)
Minimum size of a UMI cluster.
integer
1
Medaka model (-m) to use according to the basecaller used.
string
https://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g303_model.hdf5
Parameters used for alignment processes
Aligner program to use.
string
Provide the same protospacer sequence for all samples. Will override protospacer sequences provided by an input samplesheet.
string
^[ACGTacgt]+$
Parameters to use in Vsearch processes
Vsearch minimum sequence length.
integer
55
Vsearch maximum sequence length.
integer
57
Vsearch pairwise identity threshold.
number
0.99
Parameters used for functional genomic screenings
sgRNA and targetting genes, tab separated
string
^\S+\.(tsv|txt)$
Sequencing adapter sequence to use for trimming on the 5’ end
string
Sequencing adapter sequence to use for trimming on the 3’ end
string
Library in fasta file format in case you want to map with bowtie2 and then MAGeCK count
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
string
Design matrix used for MAGeCK MLE to call essential genes under multiple conditions while considering sgRNA knockout efficiency
string
control-sgrna file for MAGeCK MLE
string
Comma-separated file with the conditions to be compared. The first one will be the reference (control)
string
Parameter indicating if MAGeCK MLE should be run
boolean
Parameter indicating if MAGeCK RRA should be run instead of MAGeCK MLE.
boolean
Parameter indicating if BAGEL2 should be run
boolean
Parameter indicating if DrugZ should be run
boolean
Please provide your count table if the mageck test should be skipped.
string
^\S+\.(tsv|txt)$
sgRNA library annotation for crisprcleanR
string
a filter threshold value for sgRNAs, based on their average counts in the control sample
number
30
Minimal number of different genes targeted by sgRNAs in a biased segment in order for the corresponding counts to be corrected for CRISPRcleanR
number
3
Core essential gene set for BAGEL2
string
https://raw.githubusercontent.com/hart-lab/bagel/master/CEGv2.txt
Non essential gene set for BAGEL2
string
https://raw.githubusercontent.com/hart-lab/bagel/master/NEGv1.txt
Essential genes to remove from the drugZ modules
string
\\S+
Specify to run the Hitselection algorithm
boolean
Number of iterations the hit selection module should provide
number
1000
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path to the reference FASTA file. Will override reference sequences provided by an input sample sheet.
string
^\S+\.fn?a(sta)?(\.gz)?$
Do not load the iGenomes reference config.
boolean
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email address for completion summary, only when pipeline fails.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Send plain-text email instead of HTML.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/