Home

Welcome to the nf_genomics_pipelines wiki!

This page contains the basic information to run the workflows (or pipelines) included in this repository. All pipelines are based on Nextflow https://www.nextflow.io/. Each of the workflows has its own page where the specifics of each of the pipelines is explained.

Please note that this is a work in progress and maturity status of each of the pipelines described here is different.

Alignment files (BAM files)

This subsection contains the documentation for pipelines analysing the alignment files in the BAM, CRAM format:

• cov_per_base.nf
• convert2bam.nf

VCF files

This subsection contains the documentation for pipelines manipulating VCF files

• normalization.nf
• split_into_chros.nf

File handling

File tracking

This subsection contains documentation on pipelines used for file tracking, i.e. calculating MD5s:

• run_md5.nf

File downloading

This subsection contains documentation on pipelines used for file downloads, i.e. downloading files from the European Nucleotide Archive (ENA)

• downloadFromENA.nf