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).
2.1.0). The latest
stable release is
2.3.0
.
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.
booleanParameters regarding umi molecular identifiers (UMIs)
Minimum size of a UMI cluster.
integer1Medaka model (-m) to use according to the basecaller used.
stringr941_min_high_g360Parameters 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.
stringParameters 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
Design matrix used for MAGeCK MLE to call essential genes under multiple conditions while considering sgRNA knockout efficiency
stringComma-separated file with the conditions to be compared. The first one will be the reference (control)
stringPlease provide your count table if the mageck test should be skipped.
string^\S+\.(tsv|txt)$sgRNA and targetting genes, tab separated
string^\S+\.(tsv|txt)$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.txtReference 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)?$Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
booleantrueShow all params when using --help
booleanBy 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
stringgenomesValidation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.