Authors: Lasse Faber, Martin Hölzer
Treat your assemblies well!
A pipeline combining docker containers or conda environments and nextflow for the evaluation of (de novo) transcriptome assembly results.
To see all options:
nextflow run main.nf --help
Simple example execution:
nextflow run main.nf --assemblies 'test_data/*.fasta' --reads test_data/eco.fastq --reference test_data/eco_genome.fa --annotation test_data/eco_annotation.gff3 --threads 8 --busco bacteria_odb9 -profile standard
The workflow can be deployed in different environments.
- standard: uses docker containers and can be run locally
- conda: uses conda environments and can be run locally
- googlegenomics: uses the google cloud and needs to configured manually to run with your gcloud environment
This workflow implementation was motivated by our study comparing various de novo transcriptome assembly tools: