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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringOutput intermediate files, including specific prediction lists.
booleanfalseEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
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.
booleanfalseIf set to true, the pipeline will use all ortholog search methods.
Use local databases for the analysis.
booleanfalseIf set to true, the pipeline will use local databases for the analysis.
Run the pipeline in offline mode. Overrides all online database flags.
booleanfalseIf set to true, the pipeline will run in offline mode. local_databases must be set separately.
Skip using OMA for the ortholog search.
booleanfalseIf set to true, the pipeline will not use OMA for the ortholog search.
Path to the OMA database.
stringIf local_databases is set to true, the pipeline will use this path to the OMA database.
Path to the Uniprot-OMA ID map.
stringIf local_databases is set to true, the pipeline will use this path to the OMA-Uniprot ID map.
Path to the Ensembl-OMA ID map.
stringIf local_databases is set to true, the pipeline will use this path to the OMA-Ensembl ID map.
Path to the RefSeq-OMA ID map.
stringIf local_databases is set to true, the pipeline will use this path to the OMA-RefSeq ID map.
Skip using PANTHER for the ortholog search.
booleanfalseIf set to true, the pipeline will not use PANTHER for the ortholog search.
Path to the PANTHER database.
stringIf local_databases is set to true, the pipeline will use this path to the PANTHER database.
Skip using OrthoInspector for the ortholog search.
booleanfalseIf set to true, the pipeline will not use OrthoInspector for the ortholog search.
The version of the OrthoInspector database to use.
stringEukaryota2023This SHOULD be left as the default if working with eukaryotes. Only change if working with bacteria, or an old version is required for reproducibility.
Path to the OrthoInspector database.
stringIf local_databases is set to true, the pipeline will use this path to the OrthoInspector database.
Use EggNOG for the ortholog search.
booleanfalseIf set to true, the pipeline will not use EggNOG for the ortholog search.
Path to the EggNOG database.
stringIf local_databases is set to true, the pipeline will use this path to the EggNOG database.
Path to the EggNOG ID map.
stringIf local_databases is set to true, the pipeline will use this path to the EggNOG ID map.
Skip merging IDs based on sequence.
booleanfalseIf set to true, the pipeline will skip merging the ortholog search results.
Use centroid strategy for the ortholog search. Overrides min_score.
booleanfalseIf set to true, the pipeline will use centroid strategy for the ortholog search.
Minimum score for the ortholog search.
number2The minimum score for the ortholog search. If use_centroid is set to true, this parameter will be ignored.
All options related to the downstream analysis subworkflows.
Skip the downstream analysis. Overrides all other downstream options.
booleanfalseIf set to true, the pipeline will skip the downstream analysis.
Skip report generation.
booleanfalseIf set to true, the pipeline will not generate a report. Intended for large batch processing.
Use structures for the analysis.
booleanfalseIf set to true, the pipeline will use AlphaFold structures for the analysis.
Number of bootstrap replicates for IQ-TREE.
integer1000If set to 0, bootstrap will not be performed.
Number of bootstrap replicates for FastME.
integer100If set to 0, bootstrap will not be performed.
Options to skip various steps within the workflow.
Skip the ortholog plots.
booleanfalseIf set to true, the pipeline will skip the ortholog plots.
Skip using IQ-TREE for the phylogenetic analysis.
booleanfalseIf set to true, the pipeline will not use IQ-TREE for the phylogenetic analysis.
Skip using FastME for the phylogenetic analysis.
booleanfalseIf set to true, the pipeline will not use FastME for the phylogenetic analysis.
Skip the tree plots.
booleanfalseIf set to true, the pipeline will skip the tree plots.
Skip 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/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})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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