Orthogarden requires two inputs to run, a metadata file organized as a .csv file and a configurable shell script.

The metadata file contains four columns with a header of id,r1,r2,ref. The header must be present in the file for Orthogarden to function. Samples must either be short, paired-end reads or an assembly.

The formatting must match the following, including header:

id,r1,r2,ref,augustus
taxonA,/path/to/forward.fastq,/path/to/reverse.fastq,aedes
taxonB,/path/to/forward.fastq/path/to/reverse.fastq,fly
taxonC,,,reference.fna,fly

There are currently no plans for Orthogarden to support single-end reads. The descriptions for the four columns are as follows:

id A personal identifier for a particular sample. This value must be present and unique for each sample.

r1 The file path to the forward set of short reads for a particular sample. If this sample is an assembly, leave this column blank.

r2 The file path to the reverse set of short reads for a particular sample. If this sample is an assembly, leave this column blank.

ref The file path to the assembly of a particular sample. If this sample is a set of short reads, leave this column blank.

augustus The augustus species to use for this particular sample. This value must be present for each sample.

A nextflow run command, featuring desired parameters, is required to initiate Orthogarden.

nextflow run ../orthogarden/main.nf -resume <parameters>

A description of all parameters.