Research Object Crate for Library curation BOLD

 [](https://doi.org/10.5281/zenodo.10975576) # Library curation BOLD  This repository contains scripts and synonymy data for pipelining the automated curation of [BOLD](https://boldsystems.org) data dumps in BCDM TSV format. The goal is to implement the classification of barcode reference sequences as is being developed by the [BGE](https://biodiversitygenomics.eu) consortium. A living document in which these criteria are being developed is located [here](https://docs.google.com/document/d/18m-7UnoJTG49TbvTsq_VncKMYZbYVbau98LE_q4rQvA/edit). A further goal of this project is to develop the code in this repository according to the standards developed by the community in terms of automation, reproducibility, and provenance. In practice, this means including the scripts in a pipeline system such as [snakemake](https://snakemake.readthedocs.io/), adopting an environment configuration system such as [conda](https://docs.conda.io/), and organizing the folder structure in compliance with the requirements of [WorkFlowHub](https://workflowhub.eu/). The latter will provide it with a DOI and will help generate [RO-crate](https://www.researchobject.org/ro-crate/) documents, which means the entire tool chain is FAIR compliant according to the current state of the art. ## Install Clone the repo: ```{shell} git clone https://github.com/FabianDeister/Library_curation_BOLD.git ``` Change directory: ```{shell} cd Library_curation_BOLD ``` The code in this repo depends on various tools. These are managed using the `mamba` program (a drop-in replacement of `conda`). The following sets up an environment in which all needed tools are installed: ```{shell} mamba env create -f environment.yml ``` Once set up, this is activated like so: ```{shell} mamba activate bold-curation ``` ## How to run ### Bash Although the aim of this project is to integrate all steps of the process in a simple snakemake pipeline, at present this is not implemented. Instead, the steps are executed individually on the command line as perl scripts within the conda/mamba environment. Because the current project has its own perl modules in the `lib` folder, every script needs to be run with the additional include flag to add the module folder to the search path. Hence, the invocation looks like the following inside the scripts folder: ```{shell} perl -I../../lib scriptname.pl -arg1 val1 -arg2 val2 ``` ### snakemake Follow the installation instructions above. Update config/config.yml to define your input data. Navigate to the directory "workflow" and type: ```{shell} snakemake -p -c {number of cores} target ``` If running on an HPC cluster with a SLURM scheduler you could use a bash script like this one: ```{shell} #!/bin/bash #SBATCH --partition=hour #SBATCH --output=job_curate_bold_%j.out #SBATCH --error=job_curate_bold_%j.err #SBATCH --mem=24G #SBATCH --cpus-per-task=2 source activate bold-curation snakemake -p -c 2 target echo Complete! ```

Author

Special thanks to Sujeevan Ratnasingham and the team at CBG for the creation of the BCDM data exchange format that this pipeline operates on

License

GPL-3.0

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