nf-core/fastquorum
Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
1.1.0). The latest
stable release is
1.2.0
.
See the advisory entry for more information.
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.
stringMost common options used for the pipeline
The pipeline mode to use, either ‘rd’ for R&D or ‘ht’ for High-Throughput
stringEnable when the input is duplex sequenecing.
booleanOptions for when grouping reads by UMI
Grouping strategy
stringMaximum number of edits
integerOptions for when creating consensus reads
Minimum reads to call a consensus
integer,stringMinimum input base quality
integerOptions for when filtering consensus reads
Minimum reads to keep a consensus
integer,stringMinimum consensus base quality
integerThe maximum error rate for a single consensus base
number,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)?$Path to FASTA dictionary file.
stringPath to FASTA reference index.
stringPath to BWA mem indices.
stringDo not load the iGenomes reference config.
booleanIf generated by the pipeline save the STAR index in the results directory.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringTwo-column sample renaming TSV file passed to MultiQC. First column a set of patterns, second column a set of corresponding replacements.
stringTSV file with headers passed to MultiQC.
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/