Pre-processing pipeline

[cutleraging]

Hello,

I would like to try this pipeline out but see that it does not include the steps to generate the input files, such as the BAM and VCF files. I see that the steps are indeed listed to generate these, but in order to make your pipeline more reproducible, I am wondering if you have also made a nextflow implementation of the pre-processing steps or can point to one?

Thanks,
Ronnie

[um-pdavila]

Good idea Ronnie

[mroosmalen]

We are using this "in-house" pipeline the generate the BAM and VCF files from the FASTQ files

https://github.com/ToolsVanBox/NF-IAP

We are also working on a new pre-processing pipeline at the moment