mykrobe-atlas-kmersearch-pipeline

Pipeline for generating kmersearch index for samples

Running the pipelines

An example of running the cobs index building pipeline:

nextflow run -c mykrobe-atlas-kmersearch-pipeline/nextflow/nextflow.config 
    mykrobe-atlas-kmersearch-pipeline/nextflow/build_cobs_index.nf
    --samples samples.tsv
    --image kms.simg
    --outputDir output

In addition to the parameters in above example, other parameters could be found in nextflow/build_cobs_index.nf.