nf-core/demultiplex
Demultiplexing pipeline for sequencing data
Trim adapter sequences with fastp. When false, fastp still generates QC output, but does not modify the reads.
booleantrueWhether to publish raw, untrimmed FASTQ files alongside trimmed FASTQ files. When false, only trimmed FASTQ files are published.
booleanComma-separated list of tools to skip (fastp,fastqc,kraken,multiqc,checkqc,falco,md5sum,samshee)
This parameter must be a combination of the following values:fastp, fastqc, kraken, multiqc, checkqc, falco, md5sum, samsheestringNumber of reads to subsample for contamination detection.
integer100000Path to the Kraken2 database used for contamination screening.
stringJSON-formatted schema string passed to the samshee module for samplesheet validation.
stringSchema name passed to the samshee module for samplesheet validation.
stringLocal JSON schema file passed to the samshee module for samplesheet validation.
stringWhether the Illumina samplesheet is in v1 format.
booleanDefine 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$Flowcell ID for single-flowcell runs.
stringPath to the flowcell SampleSheet.csv for single-flowcell runs.
string^\S+\.csv$Lane number for single-flowcell runs.
integerRun directory (or tar.gz) for single-flowcell runs.
stringPer-flowcell manifest file for single-flowcell fqtk runs.
string^\S+\.csv$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringWhether to publish optional outputs such as undetermined FASTQ files.
booleanEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOptions for demultiplexing.
Demultiplexer to use.
stringOptions to customize downstream csv creation
Specifies the strandedness of RNA-Seq data for downstream sample sheet generation. This parameter does not affect the demultiplexing process but is used to generate the appropriate field in the nf-core/rnaseq samplesheet
stringParameters 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.
stringPath to the checkqc config yml file.
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.
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.
booleanCustom 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.
stringWhether to remove adapter information from the Illumina samplesheet before demultiplexing. If it is present, demultiplexers may trim adapters during the demultiplexing step.
booleantrueBoolean 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/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringDisplay the help message.
boolean,stringDisplay the full detailed help message.
booleanDisplay hidden parameters in the help message (only works when –help or –help_full are provided).
boolean