nf-core/scnanoseq
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
1.0.0). The latest
stable release is
1.2.0
.
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to GTF file.
string^\S+\.gtf(\.gz)?$Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleantrueOptions related to processing fastqs
The amount of lines to split the FASTQ into.
integerOptions to choose trimming criteria and software.
Choose minimum read length.
integer1Choose minimum average read quality score.
integer10Skip quality trimming step.
booleanOptions related to the barcode and umis.
User-provided file containing a list of cellular barcodes. Using this parameter will override the default whitelists provided by the pipeline and use the user-provided one instead.
stringSpecify the format for the barcode+umi. This parameter also defines a default barcode whitelist for the pipeline to use for barcode calling, this can be overidden with the ‘whitelist’ parameter.
stringOptions related to minimap2.
Library strandness option.
stringMinimizer k-mer length.
integer14Save secondary alignment outputs.
booleanIndicate whether to include introns in the count matrices
booleantrueOptions to skip various steps within the workflow.
Skip all QC.
booleanSkip FastQC.
booleanSkip Nanoplot.
booleanSkip ToulligQC.
booleanSkip NanoComp from FASTQ file(s).
booleanSkip NanoComp from BAM file(s).
booleanSkip RSeQC.
booleanSkip Seurat QC.
booleanSkip saving minimap2 index.
booleanSkip umi dedup.
booleanSkip MultiQC.
booleanParameters 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/masterInstitutional 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.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$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.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom 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
booleanValidation of parameters fails when an unrecognised parameter is found.
booleanValidation of parameters in lenient more.
booleanBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/