Configuration

Configuration file

The config_template.yaml file provided with this repo has all available configurable options. Short explanations are provided as commented blocks for each option.

A configuration file for the workflow must be available as config/config.yaml. You can either copy the config_template.yaml and rename it to config.yaml or make your edits straight on the template and rename it to config.yaml.

All fields included in the template must be specified, unless otherwise stated in the comment.

Sample sheet

Samples to analyze are specified within a tabular file. Path to this file should be in the sample_sheet section of the above configuration file. The structure should be as follows:

$ cat samples.tsv
analysis_id	sample_id	fasta
my_analysis	sample_1	/path/to/sample_1/sample_1.fasta
my_analysis	sample_2	/path/to/sample_2/sample_2.fasta
my_analysis	sample_3	/path/to/sample_3/sample_3.fasta

Columns names should be analysis_id, sample_id and fasta. The current workflow accepts multiple samples under sample_id, but only one analysis name under analysis_id. Input FASTA files under fasta can have any extension and/or be zipped.