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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringOutput intermediate files, including specific prediction lists.
booleanfalseEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
booleanfalseUse local databases for the analysis.
booleanfalseRun the pipeline in offline mode. Overrides all online database flags.
booleanfalseSkip using OMA for the ortholog search.
booleanfalsePath 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.
booleanfalsePath to the PANTHER database.
stringSkip using OrthoInspector for the ortholog search.
booleanfalseThe version of the OrthoInspector database to use.
stringEukaryota2023Path to the OrthoInspector database.
stringUse EggNOG for the ortholog search.
booleanfalsePath to the EggNOG database.
stringPath to the EggNOG ID map.
stringUse centroid strategy for the ortholog search. Overrides min_score.
booleanfalseMinimum score for the ortholog search.
number2All options related to the downstream analysis subworkflows.
Skip the downstream analysis. Overrides all other downstream options.
booleanfalseSkip report generation.
booleanfalseUse structures for the analysis.
booleanfalseNumber of bootstrap replicates for IQ-TREE.
integer1000Number of bootstrap replicates for FastME.
integer100Options to skip various steps within the workflow.
Skip the ortholog plots.
booleanfalseSkip using IQ-TREE for the phylogenetic analysis.
booleanfalseSkip using FastME for the phylogenetic analysis.
booleanfalseSkip the tree plots.
booleanfalseSkip 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.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay 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
booleantrueShow all params when using --help
booleanValidation of parameters fails when an unrecognised parameter is found.
booleanValidation of parameters in lenient more.
booleanBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/