In the absence of a bed file the pipeline should run on the full reference genome

[mfoll]

bedtools has a function makewindows that can create a bed from a fasta index file with windows of a given size. For example split the whole genome in 10Mb regions:

bedtools makewindows -g reference.fasta.fai -w 10000000

I could actually also use this function to split the bed instead/in combination with my own R script.

[mfoll]

We could use conditional processes like here

[mfoll]

The window size should be automatically calculated from nsplit and the total size of the genome It's easy to get from the fai file with Rscript in bash for example to cut the genome in 500:

windows_size=$(Rscript -e "cat(sum(as.numeric(read.table(\"reference.fasta.fai\")[,2]))/500,\"\n\")")
echo $windows_size
6191388

So in nextflow script it will appear as:

windows_size=$(Rscript -e "cat(sum(as.numeric(read.table(\"!{fasta_ref_fai}\")[,2]))/!{params.nsplit,\"\n\")")

[mfoll]

See https://github.com/hall-lab/speedseq#annotations