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.
string
Output intermediate files, including specific prediction lists.
boolean
false
Email 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.
string
All 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.
boolean
false
Use local databases for the analysis.
boolean
false
Run the pipeline in offline mode. Overrides all online database flags.
boolean
false
Skip using OMA for the ortholog search.
boolean
false
Path to the OMA database.
string
Path to the Uniprot-OMA ID map.
string
Path to the Ensembl-OMA ID map.
string
Path to the RefSeq-OMA ID map.
string
Skip using PANTHER for the ortholog search.
boolean
false
Path to the PANTHER database.
string
Skip using OrthoInspector for the ortholog search.
boolean
false
The version of the OrthoInspector database to use.
string
Eukaryota2023
Path to the OrthoInspector database.
string
Use EggNOG for the ortholog search.
boolean
false
Path to the EggNOG database.
string
Path to the EggNOG ID map.
string
Use centroid strategy for the ortholog search. Overrides min_score.
boolean
false
Minimum score for the ortholog search.
number
2
All options related to the downstream analysis subworkflows.
Skip the downstream analysis. Overrides all other downstream options.
boolean
false
Skip report generation.
boolean
false
Use structures for the analysis.
boolean
false
Number of bootstrap replicates for IQ-TREE.
integer
1000
Number of bootstrap replicates for FastME.
integer
100
Options to skip various steps within the workflow.
Skip the ortholog plots.
boolean
false
Skip using IQ-TREE for the phylogenetic analysis.
boolean
false
Skip using FastME for the phylogenetic analysis.
boolean
false
Skip the tree plots.
boolean
false
Skip MultiQC.
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|d|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Validation of parameters fails when an unrecognised parameter is found.
boolean
Validation of parameters in lenient more.
boolean
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/