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

nf-core

Can I raise awareness of this BWA_INDEX issue here?
Is there a way to solve this case without touching the nf-core module??
<https://github.com/nf-core/modules/issues/8720>

Can you use the `saveAs:` function of the `publishDir` directive to rename the directory?

```        publishDir = [
            path: { "${params.outdir}/bwa_indexes" },
            mode: params.publish_dir_mode,
            saveAs: { filename -&gt; filename.equals('bwa') ? "${meta.id}_bwa_index" : null }
        ]```

Hopefully this gets easier with the new publishing method, once it's finalised

I would go with just modifying the path as James described

Depends on the desired output schema - if you modify the path you get a directory with a directory inside it called `bwa` , if you set `saveAs` you rename `bwa` instead

thank you all for the  pointers :heart_hands:
I'll give it a try

worked like a charm. thanks! <@U03R5TJ77GF>