PR checklist

Closes mkfastq fails on AWS Batch #281

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

Description of error reported:

cellranger/mkfastq process fails when running nf-core/demultiplex on AWS Batch with -profile test_mkfastq,docker.
When running locally, the output folders are created (but without files) hence the process ends succesfully. When running on AWS Batch the process fails with the following error:

Missing output file(s) `*_outs/outs/fastq_path/Reports` expected by process `NFCORE_DEMULTIPLEX:DEMULTIPLEX:MKFASTQ_DEMULTIPLEX:CELLRANGER_MKFASTQ (test_sample.1)`

Some explanation may come from the following AWS doc explaining that S3 is a flat system where files are grouped by common prefixes to simulate folders. It also explains that the S3 folders behave differently than local systems. So, uploading an empty folder to S3 may be the cause of the error reported by @KallyopeComp.

Changes

• Set reports output to optional: true.
• Set stats output to optional: true.

Notes:

• Module snapshot was also tested.
• Module linting throws a warning related to the container version.