Orthofisher Module

Rule orthofisher_input_generation

Runs orthofisher on input files of FASTA file and pHMM paths the intake rule.

config orthofisher_hmmer_files

list of hmmer files for orthofisher

default: ['../tests/test-datat/hmms/1080at3041.hmm']

Checkpoint orthofisher

Runs orthofisher on input files of FASTA file and pHMM paths the intake rule.

Conda

name: orthofisher
channels:
  - conda-forge
  - bioconda
dependencies:
  - coreutils
  - python=3.9
  - hmmer=3.3.2
  - pip
  - pip:
    - orthofisher>=1.0.4

Checkpoint min_seq_filter_orthofisher

List all the ortholog ids and puts them in a file.

Only keeps the orthologs with a minimum number of sequences. It also removes suffixes added to the IDs by orthofisher.

config ortholog_min_seqs

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

default: 5