Orthofinder Module

Rule orthofinder

Runs OrthoFinder on fasta files from the intake rule.

OrthoFinder runs to the point of orthogroup inference.

Conda

channels:
  - bioconda
  - conda-forge
dependencies:
  - orthofinder==2.5.4
  - scipy==1.8.1

Checkpoint orthogroup_classification

Classifies orthogroups as single-copy or multi-copy or rejects them for not having enough sequences or taxa.

Conda

channels:
  - conda-forge
dependencies:
  - coreutils
  - python=3.10
  - pip
  - seaborn
  - typer
  - open-fonts
  - coreutils
  - rich==12.4.1
  - joblib==1.1.1
  - plotly==5.22.0
  - python-kaleido==0.2.1
  - pip:
    - scipy==1.8.1
    - pandas==1.4.3
    - matplotlib==3.5.2

Rule orthofinder_report_components

Converts the orthofinder output to HTML components that will be used in the Orthoflow report.

Conda

channels:
  - conda-forge
dependencies:
  - coreutils
  - python=3.10
  - pip
  - seaborn
  - typer
  - open-fonts
  - coreutils
  - rich==12.4.1
  - joblib==1.1.1
  - plotly==5.22.0
  - python-kaleido==0.2.1
  - pip:
    - scipy==1.8.1
    - pandas==1.4.3
    - matplotlib==3.5.2

Rule orthosnap

Run OrthoSNAP to retrieve single-copy orthologs.

output

A directory with an unknown number of fasta files.

config orthosnap_occupancy

by default it uses ortholog_min_seqs

default: None

Conda

channels:
  - bioconda
  - conda-forge
dependencies:
  # WARNING: The below versions **must** match the dependencies of orthosnap to allow the build to work on M1 macs.
  - numpy=1.20.1
  - mafft=7.520 
  - fasttree=2.1.11
  - pip
  - pip:
    - orthosnap==1.1.0

Checkpoint orthofinder_all

Collects all the SC-OGs and the SNAP OGs and creates symlinks for each in a single directory.

config ortholog_min_seqs

Minimum number of sequences that needs to be in an alignment for it to proceed to phylogenetic analysis

default: 5