Using FASTA_GXF_BUSCO_PLOT sub workflow

[GallVp]

Hello Team!

I built a reusable sub workflow for performing BUSCO on genome alone, or on genome and annotation. I have used it in two other pipelines. It is currently sitting in my own modules repo: https://github.com/GallVp/nxf-components/blob/7188d37139f8dbdfd73cbfb5b0e3f811d1993392/subworkflows/gallvp/fasta_gxf_busco_plot/main.nf#L7

I think we should be sharing this across pipelines. I can submit it to nf-core/modules and add it here. Checking if there is interest here and if there is need to modify it to suite the needs of this pipeline?

• Mentions, @FernandoDuarteF , @chriswyatt1, @stephenturner
• nf-core issue: new subworkflow: FASTA_GXF_BUSCO_PLOT modules#5584
• Other pipelines using it:
  • https://github.com/Plant-Food-Research-Open/assemblyqc/blob/cec2728d0785d97e0e9493558c83d83d0b48240e/workflows/assemblyqc.nf#L442
  • https://github.com/Plant-Food-Research-Open/genepal/blob/24a8f50e241105b98c88035fd9c2a0cad8ff728f/workflows/genepal.nf#L206

[chriswyatt1]

That looks really useful, will check it out next week.

[FernandoDuarteF]

I think we should definitively incorporate this to our pipeline.

I was also thinking we should make genome.nf and genome_and_annotation.nf into workflows, as right now they are subworkflows.

[FernandoDuarteF]

We should also have a look at the BUSCO subworkflow from the MAG pipeline. See #85.

[GallVp]

We should also have a look at the BUSCO subworkflow from the MAG pipeline. See #85.

My implementation does have a val_busco_lineages_path input. If this is provided, busco will download the data there once and will reuse it. If all the data is already downloaded, then busco will use that instead of redownloading it.

For cloud environments, this parameter needs to be optimised so that a tar ball can be passed similar to what mag is doing.

[FernandoDuarteF]

Hi @GallVp, I would like to incorporate your BUSCO subworkflow into our pipeline, at least for now. We can update it later once it's made into an nf-core subworkflow.

I'm not sure what's the etiquette to follow here, especially when it comes to giving you proper credit.

[GallVp]

Thank you @FernandoDuarteF

It will be good to share the workflows across pipelines and maintain them jointly. I am happy to create a PR and that will put me as a contributor on the repo. That's enough credit for me. How about we do the following,

• I submit the sub-workflow to nf-core/modules and invite your review. Hopefully, it will be accepted now that there are two pipelines using it. If not, we will have to maintain it where it is, i.e. in my modules repo.
• I create a PR to genomeqc for adding the sub-workflow and again invite your review.

[FernandoDuarteF]

Thank you @GallVp! Awesome, let's do that then.