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Detailed Flag explanation

Run option

  • by default WtP deploys only a selection of phage prediction tools that was benchmarked by Ho et al.
  • if you wish to run all integrated phage prediction tools: 
`--all_tools` # activate all included phage prediction tools

Inputs

  • Input examples:
  • wildcards need single quotes around the path (')
--fasta /path/to/phage-assembly.fa  # path to your fasta-file
--fasta '/path/to/*.fa'             # path to all .fa files in a dir

Profiles

  1. Choose the environment: local, slurm, lsf or ebi
  2. Choose the engine: docker or singularity
  3. examples:
-profile local,docker
-profile local,singularity
-profile lsf,docker

Custom phage annotation database

--annotation_db will allow you to provide your own database instead of the default pvog database

  • you need the following file types for the annotation process (hmmscan),
needed files
custom.hmm
custom.hmm.h3f
custom.hmm.h3i
custom.hmm.h3m
custom.hmm.h3p
  • tar -czvf custom_db.tar.gz custom.hmm custom.hmm.h3f custom.hmm.h3i custom.hmm.h3m custom.hmm.h3p
  • with --annotation_db custom_db.tar.gz you can provide your own custom phage annotation database

Release candidate

  • A release candidate is a released version of WtP which ensures proper functionality
  • version control ensures reproducibility as each tools version is also "locked" within the release candidate
  • databases have no automatic version control (they are downloaded from the source)
  • if you need version control for databases, just make a copy of the database dir after download
  • you can specify the database dir via the --database flag (see below)
  • WtP only downloads a database if it's missing, it is not "auto-updating" them
  • add this flag to your command and a specific release is used instead
-r v1.1.0

Data handling

  • WtP handles everything by default
  • If you need to change paths use the following commands
  • It's useful to specify --workdir to your current working dir if /tmp (default) has limited space
-work-dir /path/to/dir    # defines the path where nextflow writes temporary files, default: '/tmp/nextflow-phage-$USER'
--databases /path/to/dir  # specify download location of databases, default './nextflow-autodownload-databases'
--cachedir /path/to/dir   # defines the path where singularity images are cached, default './singularity-images'
--output results          # path of the outdir, default './results'

Pre-download for Offline-mode

  • --setup skips analysis and just downloads all databases and containers
  • Needs roughly 30 GB storage for databases, excluding programs

nextflow run replikation/What_the_Phage --setup -r v1.1.0 -profile singularity,local

  • you can change the database download location via (--databases)
  • make sure that you specify the database location when executing WtP, if you change the default path
  • singularity images sometimes fail during building, just try to re-execute --setup
  • WtP attempts to build images up to 3 times, image building is individually skipped if present