Introduction

dessimozlab/nf-oma-browser-build is a nextflow pipeline for building an OMA Browser instance from an OMA (Orthologous MAtrix) analysis. The pipeline converts the output of either a production OMA run or a FastOMA run into the HDF5 files needed to run a omabrowser webserver. The pipeline integrates a lot of additional data, i.e. GO annotations, domain annotations and cross-references to uniprot and refseq. Furthermore, the pipeline annotates the OMA Hierarchical Orthologous Groups (HOGs) and the OMA Groups with descriptions, computes HOG Profiles, infers Gene Ontology annotations for HOGs and reconstructs ancestral synteny, i.e. HOG orders.

All of this data can be interactively analysed with the OMA Browser web interface using a docker compose setup on the user's computer.

Pipeline summary

First part of the pipeline is dependent on input, i.e. production / FastOMA. The later steps are common to both input types.

From production OMA pipeline:

1. extract genomes in dataset from Matrix file
2. extract from genome dbs relevant data such as proteins, locus, etc
3. convert Matrix, extract splicing information

From FastOMA:

1. extract species tree, import proteomes and taxonomy
2. include additional species information from species_info file

After the initial steps, the pipeline continues with the common part.

Common part

4. convert HOGs, sequences into HDF5 database, build suffix index and kmer-lookup table (in subworkflow IMPORT_HDF5)
5. import domain annotations if available
6. import cross-references from UniProt and RefSeq (subworkflow GENERATE_XREFS)
7. import GO annotations and Ontology
8. infer keywords and fingerprints for HOGs and OMA Groups
9. compute and import HOG profiles (with HogProf)
10. infer ancestral GO annotations for HOGs (with HogProp)
11. infer ancestral synteny (with edgehog)

The pipeline produces in the end in the outputDir (default results/) the necessary files to be loaded into a docker-compose managed omabrowser instance.

Running the pipeline

The pipeline can be run with the following command:

nextflow run . -profile <profiles> [-work-dir </path/to/shared/scratch/space>] ([--<parameter> <value>]* | -params-file <paramters_file>)

We recommend to use the docker or singularity profile. And we try to support all the nf-core institutional profiles as well. Extra configurations can also be provided using the -c flag in nextflow to load your own configuration file.

Instead of specifiying the parameters on the command line, you can also provide a parameter file with the -params-file option. This file can even be generated interactively with the nf-core pipelines create-params-file command.

As an example, one can run the pipeline with a small test dataset using the following command:

nextflow run . -profile docker,test

Parameters

All parameters are listed together with a brief description by running the workflow with the --help flag:

nextflow run . --help

Below, we list in a slightly extended form the parameters that are specific to the pipeline. The parameters are grouped by the kind of input data they are related to. (These tables can be generated with nf-core pipelines schema docs -x markdown)

Convert OMA run into OMA Browser release

Datatype setting

Parameter	Description	Type	Default	Required
oma_source	Selection of OMA data source. Can be either 'FastOMA' or 'Production'. The selection requires setting either the parameters for FastOMA or Production.	string	FastOMA

FastOMA Input data

Input files generated with FastOMA

Parameter	Description	Type	Default	Required
fastoma_species_tree	Species Tree in newick format. We recommend using the tree stored in the FastOMA output folder named 'species_tree_checked.nwk'.	string
fastoma_proteomes	Folder where the input fasta files for each proteomes are located.	string
fastoma_speciesdata	TSV file with additional information about the proteomes, must contain "Name" column if provided. Help Optional (but recommended) TSV file with additional information about the proteomes. If specified, the file must contain at least the column "Name". It's values must match the filenames of the proteomes (without file extension). We suggest to include the following columns in addition: - NCBITaxonId (needed to map cross-references reliably)	string

Production OMA Input data

Input files genereated from an OMA Production run

Parameter	Description	Type	Default	Required
pairwise_orthologs_folder	Pairwise Orthologs (only by Standard OMA pipeline)	string
matrix_file	OMA Groups file	string
hog_orthoxml	Hierarchcial orthologous groups (HOGs) in orthoxml format	string		True
genomes_dir	Folder containing genomes	string		True

Domain data

File paths for domain annotations

Parameter	Description	Type	Default	Required
cath_names_path	File containing CATH domain descriptions	string	http://download.cathdb.info/cath/releases/latest-release/cath-classification-data/cath-names.txt
known_domains	Folder containing known domain assignments files	string
pfam_names_path	File containing Pfam descriptions	string	https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz

Crossreferences

Integrate crossreferences

Parameter	Description	Type	Default	Required
xref_uniprot_swissprot	UniProtKB/SwissProt annotation in text format	string	https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz
xref_uniprot_trembl	UniProtKB/TrEMBL annotations in text format	string	/dev/null
taxonomy_sqlite_path		string
xref_refseq	Folder containing RefSeq gbff files.	string

Gene Ontology

Gene Ontology files to integrate

Parameter	Description	Type	Default	Required
go_obo	Gene Ontology OBO file	string	http://purl.obolibrary.org/obo/go/go-basic.obo
go_gaf	Gene Ontology annotations (GAF format). This can the GOA database or a glob pattern with local files in gaf format.	string	https://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz

Generic options

Less common options for the pipeline, typically set in a config file.

Parameter	Description	Type	Default	Required
custom_config_version	version of configuration base to include (nf-core configs)	string	master
custom_config_base	location where to look for nf-core/configs	string	https://raw.githubusercontent.com/nf-core/configs/master