/busco2phylo-nf

Nextflow pipeline for turning a set of BUSCO results into a species tree

Primary LanguagePerl

busco2phylo-nf

Nextflow pipeline for turning a set of BUSCO results into a species tree

Dependencies

  • conda
  • nextflow

Different steps of the pipeline use mafft, iqtree and trimal.

In the example config file the environment name is orthology_env. You can create a working a environment with conda create -n orthology_env -y -c bioconda mafft iqtree trimal.

Executing the pipeline on the Sanger farm

Clone this repository:

git clone https://github.com/lstevens17/busco2phylo-nf.git

Submit an interactive job. Choose a queue appropriate to the time of execution of your pipeline. Take into account that the default config submits jobs to the 'normal' queue of 12 hours execution and if the job fails it will be resubmitted into the 'long' queue.

mbMem=5000; bsub -n 1 -q long -R"span[hosts=1] select[mem>${mbMem}] rusage[mem=${mbMem}]" -M${mbMem} -Is bash

Launch the pipeline:

nextflow -C busco2phylo-nf/busco2phylo.config run busco2phylo-nf/busco2phylo.nf --busco_dir_path [absolute_path_to_BUSCO_directory] -profile farm

Note: the busco_dir_path should contain a set of BUSCO results with sensible names. The directory name will be used to create the sequence headers in the FASTAs and therefore become the tip labels in the resulting trees.