Candidate for a Nextflow-based MVP

[GallVp]

PR checklist

• PR to nextflow_reboot branch
• conda and container directives.
• Docker container + singularity container (optional)
• Flow meta.id with each data channel
• Use nf-core resource labels such as process_high
• Used nf-core module
• Use versions.yml or versions topic
• No process in the main.nf. We can have a process in a sub-workflow file

[GallVp]

Hello @oushujun , @jguhlin

This PR includes an MVP the Nextflow-based implementation of EDTA. Currently, only two parameters are supported,

1. --genome, which can be a single Fasta or a text file listing Fastas
2. --species

I'll continue working on other parameters. But I think we need to meet in the next year and go through a couple of things,

1. Development and release workflow
2. Contribution guidelines
3. Validation
4. Documentation

[GallVp]

The test failures are related to singularity permissions issue. This might be because the PR is coming from outside this repo or because of some other repo setting. We can look at it in a meeting.

[oushujun]

OK, thank you for the great work! Let me know when you want to meet.

Shujun

[GallVp]

This has been deprecated by changes on the dev branch. For the latest Nextflow-related developments, see: https://github.com/GallVp/EDTA/tree/dev