nf-core/stableexpression
Pipeline dedicated to finding the most stable genes among a single or multiple expression dataset(s). It is useful in particular for finding the most suitable RT-qPCR reference genes for a specific species.
Define where the pipeline should find input data and save output data.
Species name.
string([a-zA-Z]+)[_ ]([a-zA-Z]+)The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringPath to comma-separated file containing information about the input count datasets and their related experimental design.
string^\S+\.csv$Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOptions for fetching datasets from Expression Atlas.
Automatically etches Expression Atlas accessions for this species. and downloads the corresponding count datasets and experimental designs.
booleanKeywords (separated by commas) to use when retrieving specific experiments from Expression Atlas.
string([a-zA-Z,]+)Provide directly Expression Atlas accession(s) (separated by commas) that you want to download.
string([A-Z0-9-]+,?)+Options for mapping gene IDs.
Skip g:Profiler ID mapping step.
booleanPath to comma-separated file containing custom gene id mappings. Each row represents a mapping from the original gene ID in your count datasets to the ensembl ID in g:Profiler.
string^\S+\.csv$Path to comma-separated file containing custom gene metadata information. Each row represents a gene and links its ensembl gene ID to its name and description.
string^\S+\.csv$Statistical options for normalisation and calculation of gene expression variation.
Tool to use for normalisation.
stringNumber of candidate genes to keep in the final list.
integer1000Threshold for KS p-value for considering samples counts as a uniform distribution.
numberParameters 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})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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.
string