A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Copying all inputs? Or just the taxonomy files?

```    custom_db = custom_library_dir ? "mkdir ${prefix} && cp -rL library taxonomy ${custom_seqid2taxid} ${prefix}" : ""
                                                          ^
    run_cleanup = keep_intermediate ? "" : """
    find -L ${prefix} -type f \\
        -not -name "*.kdb" \\
        -not -name "*idx" \\
        -not -name "taxDB" \\
        -not -name "*.counts" \\
        -delete && \\
    find -type d -empty -delete
    """```
I'll push the draft PR.

<https://github.com/nf-core/modules/pull/11607>

What's the other mode of use for this module. I'm confused by the
```    custom_db = custom_library_dir ? "mkdir ${prefix} &amp;&amp; cp -rL library taxonomy ${custom_seqid2taxid} ${prefix}" : ""```
line. `custom_library_dir` is the primary input, so it should always be there right?

And there's no nf-test for it for it being empty.

Ahhhh it might be that it you don't supply the fastas in the premade directory structure, it will download refseq or genbank by default?

Maybe the pattern was copied form another module ...