Configuration

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 for the workflow must be available as a config.yaml within the config directory. A separate my_config.yaml overriding the default options can be supplied at runtime, e.g.

$ snakemake --configfile=path/to/my_config.yaml \
<rest of snakemake options>

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.

Input data

The tools wrapped in this workflow expect phage sequences as input. You should try to make sure that the input sequences you want to analyze correspond to phage genomes/contigs (or at least viruses).

A separate workflow to identify phage/viral genomes/contigs is What the Phage.

The current workflow can handle multiple samples. For each sample, all viral contigs to be analyzed should be provided as a single multifasta (can be gz-ipped). A mapping between sample ids and their corresponding fasta file is provided as a samplesheet, as described below.

Sample sheet

You must define a samplesheet with two tab (\t) separated columns. The header line must contain two fields, sample    fasta. Values from the sample column must be unique and are used as sample identifiers. Their corresponding fasta values must be valid paths to (multi)fasta files with the phage sequences for that sample.

An example:

$ cat samples.tsv
sample      fasta
s01 /path/to/s01.fna
s02 /path/to/another.fna.gz

Note

There is no need to follow any convention for the fasta file name to reflect the sample id. The values in the sample column are the ones to worry about, as these are the ones used as wildcards within the Snakefile.

You can either fill in the location of the samplesheet within the config/config.yaml. or use snakemake’s --config samplesheet=/path/to/my_samples.tsv mechanism when executing the wofkflow.

Running specific tools

You can select which tools to run with the tools configuration option. For example, if you only want to run RaFaH and HTP you can specify them as a list for the tools configuration field

tools:
    - rafah
    - htp

This will skip the execution of the rest of the tools. Note that this list is inclusive, meaning tools specified here will be executed.

The string all can be specified to run all tools (default behavior)

tools: all