MethylScore-nf

A nextflow implementation of Computomics' MethylScore pipeline

Usage

Setting up the environment

The only software dependencies that are required to run MethylScore are nextflow, and one of the following: Singularity, Docker, Charliecloud or Podman.

Running the pipeline

To run the pipeline, you have to provide atleast --SAMPLE_SHEET and --GENOME (same as the one which you mapped the reads against)

nextflow run Computomics/MethylScore --SAMPLE_SHEET=/path/to/samplesheet.tsv --GENOME=/path/to/reference_genome.fa -profile cbe,singularity

Parameters

Pipeline parameters are initialized to their default values.

Individual parameters can be passed to the pipeline on the commandline. For example if you want methylated regions to be visualized as IGV tracks:

nextflow run Computomics/MethylScore --SAMPLE_SHEET=/path/to/samplesheet.tsv --IGV -profile cbe,singularity

Alternatively, the repository also contains an example_config.yaml, which can be used to pass custom parameters to the pipeline using the -params-file flag.

nextflow run Computomics/MethylScore -params-file=/path/to/config.yaml

Profiles

There are three profiles which use different methods to (automatically) resolve external pipeline dependencies. Note that you have to provide one of them with the -profile flag.

Singularity -profile singularity or Charliecloud -profile charliecloud

The Singularity and Charliecloud profiles uses a prebuilt container that includes all dependencies needed to run the pipeline.

Docker or Podman -profile docker or -profile podman

While these are very similar to Singularity or Charliecloud, they are usually not available in Cluster environments. They are nevertheless very useful for local runs of the pipeline.

Note: with -profile local,docker -profile local,podman you can easily run the pipeline on your local computer, given you have nextflow and Docker or Podman installed.

Cluster specific profiles

CBE -profile cbe

This profile is optimized for the CLIP Batch Environment (CBE) at the Vienna BioCenter and uses singularity by default. Enable with -profile cbe.