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NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.
https://www.earthbiogenome.org/
GNU General Public License v3.0
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New Module: BLOBTOOLKIT #5

Open mahesh-panchal opened 2 years ago

mahesh-panchal commented 2 years ago

Which tool should be included? blobtoolkit

How is it used? The toolkit is a Snakemake Workflow which uses blobtools2.

snakemake -p \
                     --use-conda \
                     --conda-prefix /blobtoolkit/.conda \
                     --directory /blobtoolkit/data \
                     --configfile /blobtoolkit/data/$ASSEMBLY.yaml \
                     --stats $ASSEMBLY.snakemake.stats \
                     -j $THREADS \
                     -s /blobtoolkit/insdc-pipeline/Snakefile \
                     --resources btk=1

Pipeline instructions are here

Which workflow should it be included in? Assembly validation.

mahesh-panchal commented 2 years ago

Docker images are extremely large(~ 2.24GB ) : https://hub.docker.com/r/genomehubs/blobtoolkit/tags meaning a lot of space is needed for conversion to singularity.

mahesh-panchal commented 2 years ago

https://blobtoolkit.genomehubs.org/pipeline/pipeline-tutorials/running-the-pipeline-in-a-container/ doesn't work. There's no Snakefile in the container.

mahesh-panchal commented 1 year ago

Sanger is implementing it now: https://github.com/sanger-tol/blobtoolkit. It could be potentially included as a submodule subworkflow (see https://github.com/mahesh-panchal/test_nfcore_workflow_chain ).