nf-core/demultiplex
Demultiplexing pipeline for sequencing data
1.5.4). The latest
stable release is
1.6.1
.
Whether or not to skip trimming
booleantrueComma-separated list of tools to skip (fastp,fastqc,kraken,multiqc,checkqc,falco,md5sum,samshee)
string[]Number of reads to subsample for contamination detection.
integer100000Path to Kraken2 DB to use for screening
stringString in JSON format to be passed to samshee module for samplesheet validation
stringSchema name to be passed to samshee module for samplesheet validation
stringLocal JSON file to be passed to samshee module for samplesheet validation
stringWhether or not illumina samplesheet is v1
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
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.
string[]Less 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.
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 remove adapter information from Illumina samplesheet. If adapter information is present, the various bcl conversion tools will perform adapter trimming already at 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/