Command overview

The basic command

nextflow run \                   # calling the workflow
 replikation/What_the_Phage \    # WtP Git-Repo
 --fasta /path/to/file.fa \      # provide a fasta-file as input
 --cores 8 \                     # number of cores you want to use
 -profile local,docker           # choose the environment:local and docker
 -r v1.2.0                       # WtP release version

Flag overview

Mandatory

Flag	simple explanation
--fasta	path/to/phage-assembly.fa or '/path/to/*.fa'
-profile	local,docker or local,singularity or lsf,docker
-r	v1.2.0

Options

Flag	simple explanation
--help	will show you this page in your terminal
--filter	e.g. 1500 bp (sequences below 1500 bp won't be analyzed)
--cores	e.g. 10
--setup	pre-downloads all you need to run WtP

Pathing

Flag	simple explanation
--workdir	/path/to/dir
--database	/path/to/dir
--cachedir	/path/to/dir
--output	e.g. results

Workflow control

Flag	simple explanation
--dv	deactivates deepvirfinder
--mp	deactivates metaphinder
--pp	deactivates PPRmeta
--sm	deactivates sourmash
--vb	deactivates vibrant
--vf	deactivates virfinder
--vn	deactivates virnet
--vs	deactivates virsorter
--ph	deactivates phigaro
--vs2	deactivates virsorter2
--identify	only phage identification, skips analysis
--annotate	only annotation, skips phage identification
--all_tools	activate all included phage prediction tools
--annotation_db	/path/to/your/custom_phage_annotation_db.tar.gz

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