Developing pipelines

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Trying your first Gitpod environment

You can run Gitpod with any nf-core pipeline repository.

For example, for nf-core RNA-seq pipeline, simply click the green Gitpod button or add the Gitpod prefix before the git URL (instead of https://github.com/nf-core/rnaseq, type https://gitpod.io/#https://github.com/nf-core/rnaseq).

Once Gitpod has loaded, including the container with all the tools we need, we can go to the terminal and type the following to start the nf-core workflow:

nextflow run nf-core/rnaseq \
    -profile test,docker \
    --outdir my_result

This should run the test data through nf-core rnaseq, using docker with your results in the folder: my_result. This will take some time to complete.

Using this Gitpod method makes it easy to run and test nf-core pipelines quickly, but it lacks the parallelization required to run real datasets.

Testing your module with nf-test

With DSL2, much of pipeline writing is spent writing reusable modules. If you enter the Gitpod environment for modules, you can run nf-test in order to debug a particular module.

You can learn more about nf-test in this nf-core bytesize talk.

Once you are in the environment, try running an example nf-test for an existing module:

nf-test test --tag <module_name> --profile docker