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jguhlin / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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Add main.nf into the new branch #4

Closed jguhlin closed 3 months ago

jguhlin commented 3 months ago

@GallVp Shortened main.nf, let me know if I should trim it a bit more.

GallVp commented 3 months ago

@jguhlin

That's good. Let's get this running with CONDA. Can you please add the fffx to bin, a minimal nextflow.config and a test command as comment in the main.nf which runs this short workflow on your computer using CONDA. I'll try to modify it to work with docker/singularity.

jguhlin commented 3 months ago

@GallVp I can do a static compile and put that into bin, but unless I put it in bioconda (planning to do it eventually anyways). But right now there's nothing from conda it needs to run.

Will get the test command tomorrow.

GallVp commented 3 months ago

@GallVp I can do a static compile and put that into bin, but unless I put it in bioconda (planning to do it eventually anyways). But right now there's nothing from conda it needs to run.

Will get the test command tomorrow.

Static compile for Linux + x86 will do. Unless you are on windows. Can you cross compile?

jguhlin commented 3 months ago

On linux, can cross compile to whichever platform and CPU is needed.

GallVp commented 3 months ago

On linux, can cross compile to whichever platform and CPU is needed.

Bioconda is one option. Another option is that we compile it for Linux + x86 or Linux + amd64 and then use a conda environment which provides Rust dynamic libraries or maybe even that can be skipped with a static compile? But for Linux and macOS with other machine architectures such as arm8, etc. we include a ubuntu docker container. Docker can emulate amd64. This approach is similar to this module: https://github.com/Plant-Food-Research-Open/assemblyqc/blob/690e56b3d349ee32754c9cc1cfc5474308f682ee/modules/local/assemblathon_stats.nf#L6 which executes a perl script from bin but inside a standard ubuntu container.

GallVp commented 3 months ago

Hi @jguhlin

I have added the CI action. Other changes include.

  1. A minimal nextflow.config to list available profiles.
  2. A cleanNXF script which clean up the current directory after a Nextflow run
  3. A params.outdir parameter which can be used as a suffix for all results.
jguhlin commented 3 months ago

@GallVp Great. I'll merge this one and start on that step.

I'll also get some CI testing going for https://github.com/jguhlin/fffx-tools