Addition of miRDeep2 program for the detection of novel miRNAs

[lcabus-flomics]

Many thanks to contributing to nf-core/smrnaseq!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

PR checklist

This pull request is for the addition of miRDeep2 program for the detection of novel miRNAs. It is not included for downstream analysis. There is also an addition of a skip_mirdeep step to skip this program.

• This comment contains a description of changes (with reason)
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/smrnaseq/tree/master/.github/CONTRIBUTING.md

[jfy133]

A couple of minor comments/suggestions but LGTM (from perspective of someone who doesn't really know what type of data this pipeline is addressing ;) )

[lcabus-flomics]

One thing, I have changed the process.container to my own (lluccabus/smrnaseq), to add the miRDeep2 program, should I change this to the default nfcore/smrnaseq:1.0.0 and ask the owners of the container to add miRDeep2?

[jfy133]

One thing, I have changed the process.container to my own (lluccabus/smrnaseq), to add the miRDeep2 program, should I change this to the default nfcore/smrnaseq:1.0.0 and ask the owners of the container to add miRDeep2?

@apeltzer might be able to help here. However if I understand correctly, I'm pretty sure all you just need to to do is to add it to environment.yml, and then the change will be detected and the docker container will be already built.

IIRC in nf-core/eager the procedure we often use is have a separate PR for the environment.yaml bump, merge that, and then tests can run on the code in the main PR but against the new container.

[lcabus-flomics]

Okay, I have changed the environment.yml already, so I will change the process.container to nfcore/smrnaseq:dev.

[maxulysse]

LGTM

[ewels]

Failure is due to the missing pipeline schema. This is because the pipeline needs to be updated to the latest version of the template and have a new schema created using nf-core schema build.

This is kind of a big job that is separate from this PR, so I will override the failing tests and merge 👍🏻

Thanks @lcabus-flomics !