Workflow name

[elizabethmcd]

Potentially change repo and workflow name to just metagenomics-nf as when you run with nextflow run Arcadia-Science/arcadia-metagenomic-assembly-nf .... the Arcadia part is redundant in the repo/workflow name. However if you clone the repository and run with nextflow run main.nf then the repo name would just be metagenomics-nf.

It depends on what the suggested "quick start" run should be, as not requiring git clone is a faster start. Forking or cloning would more suggest that somebody is contributing changes to the pipeline and not running it persay.

The other issue is if metagenomics-nf alone is enough description, as this just covers the QC, assembly, and evaluation of metagenomic reads/assembly. It doesn't imply subsequent binning for example, which would be a separate workflow binning-nf for example under this nomenclature strategy.

@taylorreiter thoughts?

[taylorreiter]

what about metagenomics-assembly-nf? Then subsequent pipelines could include key words for what those things do (e.g. metagenomics-binning-nf and metagenomes-annotation-nf).

I agree that arcadia is redundant. I would prefer if the suggested quickstart does not involve git clone. That gets really cumbersome when the nf workflow is only one piece of a larger analysis. However, I'm still new to running nf pipelines so it's hard for me to have strong opinions here.

[elizabethmcd]

Ok I agree on metagenomics-assembly-nf for this one and metagenomics-binning-nf for the subsequent workflow. I think I will keep annotation as microbial-annotation-nf so it's clear you can input a microbial genome from any source (isolate or MAG)

[elizabethmcd]

Workflow name is changed to metagenomics to be all lower case, and one word with no punctuation. This conforms to nf-core practices when creating and naming pipelines with nf-core create, according to issues https://github.com/nf-core/tools/issues/85 and https://github.com/nf-core/tools/pull/1822