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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringType of analysis to perform. Targeted for targeted CRISPR experiments and screening for CRISPR screening experiments.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringAlternative pipeline steps to include in the targeted analysis.
Trim overrepresented sequences from reads (cutadapt)
booleanIf the sample contains umi-molecular identifyers (UMIs), run the UMI extraction, clustering and consensus steps.
booleanSkip the classification of samples by clonality.
booleanIf the step is not skipped, samples are classified into: homologous WT, homologous NHEJ or heterologous NHME.
Parameters regarding umi molecular identifiers (UMIs)
Minimum size of a UMI cluster.
integer1Medaka model (-m) to use according to the basecaller used.
stringhttps://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g303_model.hdf5Parameters used for alignment processes
Aligner program to use.
stringProvide the same protospacer sequence for all samples. Will override protospacer sequences provided by an input samplesheet.
string^[ACGTacgt]+$Parameters to use in Vsearch processes
Vsearch minimum sequence length.
integer55Discard sequences shorter than vsearch_minseqlength.
Vsearch maximum sequence length.
integer57Discard sequences longer than vsearch_minseqlength.
Vsearch pairwise identity threshold.
number0.99Do not add the target to the cluster if the pairwise identity with the centroid is lower than id. The pairwise identity is defined as the number of (matching columns) / (alignment length - terminal gaps).
Parameters used for functional genomic screenings
sgRNA and targetting genes, tab separated
string^\S+\.(tsv|txt)$Sequencing adapter sequence to use for trimming on the 5' end
stringSequencing adapter sequence to use for trimming on the 3' end
stringLibrary in fasta file format in case you want to map with bowtie2 and then MAGeCK count
stringSpecify 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
stringDesign matrix used for MAGeCK MLE to call essential genes under multiple conditions while considering sgRNA knockout efficiency
stringcontrol-sgrna file for MAGeCK MLE
stringComma-separated file with the conditions to be compared. The first one will be the reference (control)
stringParameter indicating if MAGeCK MLE should be run
booleanParameter indicating if MAGeCK RRA should be run instead of MAGeCK MLE.
booleanParameter indicating if BAGEL2 should be run
booleanParameter indicating if DrugZ should be run
booleanPlease provide your count table if the mageck test should be skipped.
string^\S+\.(tsv|txt)$sgRNA library annotation for crisprcleanR
stringa filter threshold value for sgRNAs, based on their average counts in the control sample
number30Minimal number of different genes targeted by sgRNAs in a biased segment in order for the corresponding counts to be corrected for CRISPRcleanR
number3Core essential gene set for BAGEL2
stringhttps://raw.githubusercontent.com/hart-lab/bagel/master/CEGv2.txtNon essential gene set for BAGEL2
stringhttps://raw.githubusercontent.com/hart-lab/bagel/master/NEGv1.txtEssential genes to remove from the drugZ modules
string\\S+Specify to run the Hitselection algorithm
booleanNumber of iterations the hit selection module should provide
number1000Reference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to the reference FASTA file. Will override reference sequences provided by an input sample sheet.
string^\S+\.fn?a(sta)?(\.gz)?$Do not load the iGenomes reference config.
booleanDo 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.
The base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf 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.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe 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.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/