README.md

# NeoLeg pipeline

Nextflow pipeline creating the neo4j NeoLeg database.

## Requirements
- the nextflow.config needs to be modified for your needs. Another config file can be created using nextflow.config as a template.
	- path to required files should be given as command arguments or mentionned in the config file
## Input

### species_info
File describing the species genomes (tsv format). Column header as specified in the example is mandatory.
If a field is unknown, replace with "NA" or similar.

example:
```
sp_id   sp_name accession       ncbi_taxon_id   assembly_v      annotation_v
lcul    Lens culinaris  CDC Redberry    3864    2.0     2.0
mtrun   Medicago truncatula     A17     3880    5.0     5.1.7
psat    Pisum sativum   Cameor  3888    a       c
vfab    Vicia faba      Hedin/2 3906    1.0     1.0
vrad    Vigna radiata   GCF_000741045.1 3916    Vradiata_ver6   101
```

### species_files
File listing paths to all genome files (tsv format). Column header as specified in the example is mandatory.

example
```
ID      genome  gff3    protein
lcul    input/genome/lcul_genome.fa     input/genome/lcul_annotation.gff3       input/proteins/lcul.fa
mtrun   input/genome/mtrun_genome.fa    input/genome/mtrun_annotation.gff3      input/proteins/mtrun.fa
psat    input/genome/psat_genome.fa     input/genome/psat_annotation.gff3       input/proteins/psat.fa
vfab    input/genome/vfab_genome.fa     input/genome/vfab_annotation.gff3       input/proteins/vfab.fa
vrad    input/genome/vrad_genome.fa     input/genome/vrad_annotation.gff3       input/proteins/vrad.fa
```
### annotation_files
File listing paths to all annotation files (tsv format). Column header as specified in the example is mandatory.
If eggnog files are not provided, user can replace the path by a "." and set `eggnog_files` to true in config.

example
```
ID      eggnog	mapman  interproscan    trapid_go       trapid_gene_family      trapid_rna_family
lcul    input/eggnog/lcul.tsv	/input/mapman/lcul.txt input/interproscan/lcul.tsv   input/trapid/go/lcul_go.zip   input/trapid/gene_family/lcul_gf.zip  input/trapid/rna_family/lcul_rf.zip
mtrun   input/eggnog/mtrun.tsv	input/mapman/mtrun.txt        input/interproscan/mtrun.tsv  input/trapid/go/mtrun_go.zip  input/trapid/gene_family/mtrun_gf.zip input/trapid/rna_family/mtrun_rf.zip
psat    input/eggnog/psat.tsv	input/mapman/psat.txt input/interproscan/psat.tsv   input/trapid/go/psat_go.zip   input/trapid/gene_family/psat_gf.zip  input/trapid/rna_family/psat_rf.zip
vfab    input/eggnog/vfab.tsv	input/mapman/vfab.txt input/interproscan/vfab.tsv   input/trapid/go/vfab_go.zip   input/trapid/gene_family/vfab_gf.zip  input/trapid/rna_family/vfab_rf.zip
vrad    input/eggnog/vrad.tsv	input/mapman/vrad.txt input/interproscan/vrad.tsv   input/trapid/go/vrad_go.zip   input/trapid/gene_family/vrad_gf.zip  input/trapid/rna_family/vrad_rf.zip
```

### synteny and orthology files
From OrthoFinder, need files need the Log.txt (`OF_log` parameter, for nodes annotation) and the N0.tsv (`OF_N0` parameter, file containing the orthogroups and associated genes)
From MCScanX, need the collinearity file (`synt_collinearity` parameter, is the .collinearity file).
These two sets of files can be generated using the *specifics_MCScanX* pipeline

### parameters
Some parameters are listed in the nextflow.config file.
These include but are not limited to:
- `make_eggnog_db` to select wether to create eggNOG database or use one whose path must be written in `eggnog_db` parameter
- `use_trapid_gos` if user would rather have TRAPID GOterms on RNA nodes instead of eggNOG GOterms. The `keep_hidden_gos` refers to keeping GOterms that are not the most specifics on RNAs (see http://bioinformatics.psb.ugent.be/trapid_02/documentation/general)


## Running the pipeline
```
nextflow run main.nf -c nextflow.config --species_files neoleg_infiles.tsv --annotation_files neoleg_infiles.tsv --outdir results/20220322_neoleg
```

## Output
2022/03/22
To date, the pipeline can create (if publish set to `true`) the following folders:
- *conf_files*: simple copy of config files for input tracing.
- *eggnog_annotation*: annotation of each proteome by the EggNOG database.

- *nodes_gene*: one csv file per species containing gene nodes + 1 header.
- *nodes_gene_family*: one csv file per species containing gene families nodes + 1 header. TODO: concat all of them (sort and uniq), for now doing it manually.
- *nodes_mapman*: one rdf file containing the mapman ontology for n10s import (using `n10s.rdf.import.fetch()`.
- *nodes_orthogroup*: one csv file containing all orthogroups nodes + 1 header.
- *nodes_protein*: one csv file per species containing protein nodes + 1 header.
- *nodes_protein_annotation*: one csv file per species containing protein annotation nodes from InterProScan + 1 header.
- *nodes_rna*: one csv file per species containing rna nodes + 1 header.
- *nodes_rna_family*: one csv file per species containing rna families nodes + 1 header. TODO: concat all of them (sort and uniq), for now doing it manually.
- *nodes_synteny*: one csv file containing all synteny nodes + 1 header.
- *nodes_synteny_experiment*: one csv file containing all synteny experiments nodes + 1 header.

- *edges_gene_gene_family*: one csv file per species containing edges from gene to gene family + 1 header.
- *edges_gene_orthogroup*: one csv file containing edges from gene to orthogroup + 1 header.
- *edges_gene_rna*: one csv file per species containing edges from gene to rna + 1 header.
- *edges_gene_synteny*: one csv file containing edges from gene to synteny + 1 header.
- *edges_protein_protein_annotation*: one csv file per species containing edges from protein to protein annotation + 1 header.
- *edges_rna_mapman*: one csv file per species containing edges from rna to mapman term + 1 header.
- *edges_rna_protein*: one csv file per species containing edges from rna to protein + 1 header.
- *edges_rna_rna_family*: one csv file per species containing edges from rna to rna family + 1 header.
- *edges_synteny_synteny_experiment*: one csv file containing edges from synteny to synteny_experiment + 1 header.