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]+)e.g. --species 'Arabidopsis thaliana' or --species 'homo_sapiens'
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$The dataset file should be a comma-separated file with 3 columns, and a header row. See usage docs for more information. Before running the pipeline, you will need to create a design file with information about the samples in your experiment. Use this parameter to specify its location.
Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
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.
booleanIf no Expression Atlas keywords are provided (with --eatlas_keywords) and if you want to get all Expression Atlas accessions for this species, provide this parameter.
Keywords (separated by commas) to use when retrieving specific experiments from Expression Atlas.
string([a-zA-Z,]+)The pipeline will select all Expression Atlas experiments that contain the provided keywords in their description of in one of the condition names. Example: --eatlas_keywords 'stress,flowering'
Provide directly Expression Atlas accession(s) (separated by commas) that you want to download.
string([A-Z0-9-]+,?)+Example: --eatlas_accessions 'E-MTAB-552,E-GEOD-61690'
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$The mapping file should be a comma-separated file with 2 columns (original_gene_id and ensembl_gene_id) and a header row.
Path to comma-separated file containing custom gene metadata information. Each row represents a gene and links its ensembl gene ID to its name and description.
string^\S+\.csv$The metadata file should be a comma-separated file with 3 columns (ensembl_gene_id, name and description) and a header row.
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.
integer1000Number of candidate genes to keep in the final list. These candidates genes are chosen as the ones showing the least standard variation. Default is 1000.
Threshold for KS p-value for considering samples counts as a uniform distribution.
numberP-value threshold for the Kolmogorov-Smirnov test of samples counts against a uniform distribution. Samples showing a p-value equal or below this threshold are considered not uniform and will therefore not be considered for computation of the stability score. Examples: 0, '0.05', '1E-27'. Provide a negative value to disable this filter. By default, all samples showing a pvalue of 0 will be discarded.
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/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional 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.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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