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

nf-core

I have a problem with <https://github.com/nf-core/ampliseq/pull/948>
I added a tool (I thought as usual) and I get for CI tests
`ERROR ~ Failed to publish file: /home/runner/_work/ampliseq/ampliseq/~/tests/c9d5acf2cf81a683aba1961b3c3d778c/work/50/8f8e733de5a1fc60d475327ab47ec3/decontaminated.tsv; to: /home/runner/_work/ampliseq/ampliseq/~/tests/c9d5acf2cf81a683aba1961b3c3d778c/output/decontam/decontaminated.tsv [copy] -- See log file for details`
locally it works all fine. I used here in slack the search function & googled it but didnt find a solution.
Whats unusual might be that I use `ch_decontam_metadata.subscribe{ it -> if(it.countLines() > 1) file(it).copyTo("${params.outdir}/decontam") }` (in <http://workflowsampliseq.nf|workflows/ampliseq.nf> ) and later (via config/modules.config):
```publishDir = [
            path: { "${params.outdir}/decontam" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
        ]```
maybe those two pulishing into the same directory causes the error?

Update: with singularity it works, with docker I can reproduce it also locally, that makes testing easier!

It appears like `file(it).copyTo("${params.outdir}/decontam") }` followed by a process that uses `publishDir` to copy into the same directory fails with docker but not singularity with `ERROR ~ Failed to publish file:`. I didnt find that issue in the nextflow docs or online.
Is that an nf-core template permission bug for docker? A nextflow bug? Or did I use `copyTo` inappropriate?