Pre-processing pipeline

Question

Pre-processing pipeline

cutleraging opened this issue a year ago · 2 comments

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

Answer 1 · 2023-12-05T23:08:49.000Z

Good idea Ronnie

Answer 2 · 2023-12-06T11:53:25.000Z

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