nf-core/stableexpression
This pipeline is dedicated to identifying the most stable genes within a single or multiple expression dataset(s). This is particularly useful for identifying the most suitable RT-qPCR reference genes for a specific species.
Define where the pipeline should find input data and save output data.
Scientifc species name (genus and species)
string^([a-zA-Z]+)[_ ]([a-zA-Z]+)[_ a-zA-Z]*$Output directory
stringCustom datasets (counts + designs)
string^\S+\.(csv|yaml|yml|dat)$Keywords used for selecting specific Expression Atlas / GEO accessions
string(([a-zA-Z,]+))?Only download from this platform
stringOnly get accessions from Expression Atlas / GEO and exit.
booleanOnly get accessions from Expression Atlas / GEO and download the selected datasets.
booleanEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOptions for fetching experiment data from Expression Atlas / GEO.
Skip fetching Expression Atlas accessions
booleanFetch GEO accessions from NCBI
booleanExpression Atlas / GEO accession(s) to include
string([A-Z0-9-]+,?)+File containing Expression Atlas / GEO accession(s) to download
stringExpression Atlas accession(s) to exclude
string([A-Z0-9-]+,?)+File containing Expression Atlas accession(s) to exclude
stringOptions for mapping gene IDs.
Skip g:Profiler ID mapping step
booleanTarget database for g:Profiler
stringCustom gene id mapping file
string^\S+\.(csv|dat)$Custom gene metadata file
string^\S+\.(csv|dat)$Minimum quantile for the frequency of occurrence
number0.2Minimum frequency of occurrence among all datasets
number0.1Statistical options for normalisation and calculation of gene expression variation.
Count normalisation method
stringGene length file
string^\S+\.(csv|tsv|dat)$Target distribution for quantile normalisation
stringMinimum percentage of quantile expression level
number0.2Options relative to assessment of stability for each gene.
Statistic descriptor for prior gene candidate selection. Either coefficient of variation (cv), or robust median absolute deviation (rcvm).
stringNumber of candidate genes to keep for stability scoring
integerRun Genorm
booleanWeights for stability score calculation
string^\d+(\.\d+)?,\d+(\.\d+)?,\d+(\.\d+)?,\d+(\.\d+)?$Options to improve pipeline scalability and robustness
Number of public dataset samples to choose randomly before downloading.
integerSeed for dataset random sampling.
integerParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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