A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

in the nextflow.config its set `skip_split_multiallelics    = false` and I wrong in assume that that is the default?

the params are swapped in the sub workflow vs workflow I guess.

we have WES with mt spike in so I have this in my config:

run_mt_for_wes                  = true

so the skip becomes true

<https://github.com/nf-core/raredisease/blob/12eafba3db40d76ed2f7bd27414e169ce89d3e01/workflows/raredisease.nf#L440>

            val_skip_split_multiallelics,
            val_run_mt_for_wes,

but in <https://github.com/nf-core/raredisease/blob/12eafba3db40d76ed2f7bd27414e169ce89d3e01/subworkflows/local/call_snv/main.nf>

its                     val_run_mt_for_wes            // boolean
        val_skip_split_multiallelics  // boolean