nf-core/reportho
nf-core pipeline for comparative analysis of ortholog predictions
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringOutput intermediate files, including specific prediction lists.
booleanEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringAll options related to the ortholog search subworkflow.
Use all ortholog search methods. Will mix online and local methods if needed. Overrides all individual database flags.
booleanUse local databases for the analysis.
booleanRun the pipeline in offline mode. Overrides all online database flags.
booleanSkip using OMA for the ortholog search.
booleanPath to the OMA database.
stringPath to the Uniprot-OMA ID map.
stringPath to the Ensembl-OMA ID map.
stringPath to the RefSeq-OMA ID map.
stringSkip using PANTHER for the ortholog search.
booleanPath to the PANTHER database.
stringSkip using OrthoInspector for the ortholog search.
booleanThe version of the OrthoInspector database to use.
stringEukaryota2023Path to the OrthoInspector database.
stringUse EggNOG for the ortholog search.
booleanPath to the EggNOG database.
stringPath to the EggNOG ID map.
stringSkip merging IDs based on sequence.
booleanUse centroid strategy for the ortholog search. Overrides min_score.
booleanMinimum score for the ortholog search.
number2Minimum sequence identity in Diamond
number90Minimum sequence coverage in Diamond
number80All options related to the downstream analysis subworkflows.
Skip report generation.
booleanOptions to skip various steps within the workflow.
Skip the ortholog plots.
booleanSkip MultiQC.
booleanParameters 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.
string