Nextflow modules for CLIMB-BIG-DATA. Tested using GitHub Actions and MRC-CLIMB/containers
An example pipeline using the modules is included in test-pipeline. The pipeline pulls a pair of test fastqs from the ENA, trims the fastq with trimgalore, and creates an assembly using shovill. The output files from the pipeline are published in an output directory set by params.outputDir in test-pipeline/nextflow.config
The pipeline requires a version of Nextflow that supports DSL2. To download the latest version of Nextflow:
curl -fsSL https://get.nextflow.io | bash
By default, the pipeline will just run on the local machine. To run on a cluster, modifications will have to be made to the nextflow.config to add in the executor. E.g. for a SLURM cluster add process.executor = 'slurm'. For more information on executor options see the Nextflow docs: https://www.nextflow.io/docs/latest/executor.html. Containers are defined for each process, the pipeline can be ran with docker or singularity (or other container runtimes) by adding the appropriate profiles to the nextflow.config (https://nextflow.io/docs/edge/container.html).