support remote paths in NfCoreTemplate:dump_parameters

[fbdtemme]

Currently the new dump_parameters added in v2.10 (#2425) only works on local files.
When using a remote publish dir such as s3, the json file will be written to a weird directory s3 / path / to / outdir / params_{timestamp}.json in the launchDir.
This small tweak first creates the parameter dump on the nextflow head machine as a hidden file and then moves it to the possibly remote outdir using the nextflow FilesEx helper to deal with the remote filesystems.

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[codecov]

Codecov Report

Merging #2465 (f1a99a8) into dev (a220bcd) will increase coverage by 0.00%.
The diff coverage is n/a.

❗ Current head f1a99a8 differs from pull request most recent head 5ec389e. Consider uploading reports for the commit 5ec389e to get more accurate results

@@           Coverage Diff           @@
##              dev    #2465   +/-   ##
=======================================
  Coverage   70.60%   70.60%           
=======================================
  Files          87       87           
  Lines        9437     9435    -2     
=======================================
- Hits         6663     6662    -1     
+ Misses       2774     2773    -1     

see 2 files with indirect coverage changes

[JoseEspinosa]

Thanks for reporting, I see the issue, but I was wondering why the code does not work as I copied it from here and as far as I know, we are not encountering the same issue, maybe @mirpedrol can help here...

[fbdtemme]

I have tested it again with a clean pipeline from nf-core create using the local executor but with an s3 outdir.

nextflow run . -profile test,docker --outdir s3://<bucket-name>/clean-pipeline-test --fasta genome.fa --email blah@example.com

It seems like the email code has the exact same issue. I have used the same approach to fix it there as well.

[mirpedrol]

I can't test this with S3, but code looks good, if you tested it LGTM :)