G-nom-Project/corepipeline is designed to generate core analyses for new assemblies to be added to G-nom. This includes Repeatmasker, BUSCO (genome + protein) and taXaminer (planned). The output folder can be imported instantly using the G-nom API.
Note
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.
nextflow run G-nom-Project-corepipeline/main.nf \\
--fasta <path to genomic fasta file> \\
--rmdb <path to RepeatMasker Libraries> \\
--species <species name for RepeatMasker> \\
--outdir <output directory> \\
--busco_lineage <BUSCO Lineage ID> \\
--protein_fasta <path to protein fasta file>
For BUSCO lineages please refer to the official list.
Warning
Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.
G-nom-Project/corepipeline was originally written by Lucas Koch.
We thank the following people for their assistance in the development of this pipeline:
If you would like to contribute to this pipeline, please see the contributing guidelines.
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.
This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.