nf-core/ncrnannotator
nf-core pipeline for genome-level ncRNA annotation using Infernal
Define where the pipeline should find input data and save output data.
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})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringParameters specific to the ncRNA annotation pipeline.
Not used by this pipeline. Present for nf-core schema compatibility.
stringPath to the genome FASTA file to annotate.
string^\S+\.fn?a(sta)?(\.gz)?$Annotation mode: ‘ensembl-vertebrates’ (1 Mbp chunks), ‘ensembl-invertebrates’ (100 kbp chunks), ‘mgnify-assembly’ (50 Mbp chunks, full Rfam, includes prokaryotic rRNA), or ‘full’ (1 Mbp chunks, full Rfam, eukaryotic only).
stringPath to the Rfam covariance model file (Rfam.cm).
stringPath to the Rfam seed alignment file (Rfam.seed).
stringOptional override for the Rfam accession list file.
stringGenome chunk size in base pairs for parallel cmsearch.
integerParameters 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.
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/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