Enable workflow outputs

[atrigila]

Closes #367

[atrigila]

@nf-core-bot fix linting

[atrigila]

Moving this back to draft to keep polishing the missing and extra files

[atrigila]

The mkfastq test stopped working, I think when it fetches the remote files. It will stay in Staging foreign file: https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz forever.

[atrigila]

I had to patch bcl_demultiplex because it is currently being changed / worked on to include multiqcsav. The patch will be removed and the changes will be applied in: #378

[atrigila]

The problem with sgdemux (and sgdemux's flowcell) tests:

sgdemux in this test basically reads from the fastq directory and writes the output files in the same directory:

sgdemux \
    --sample-metadata out.sample_meta.csv \
    --fastqs sim-data \
    --output-dir sim-data \
    --demux-threads 4 \
    --compressor-threads 4 \
    --writer-threads 4 \

So that's why there are some extra files:

• The files prefixed with out such as out_L001_R1_001.fastq.gz are the input fastq files.
• The files such as s10_S10_L001_R1_001.fastq.gz and s10_S10_L001_R2_001.fastq.gz are the produced output files.
• The module does not differentiate capturing between undetermined and regular fastq, so that's why undetermined fastq (such as Undetermined_S25_L001_R1_001.fastq.gz) also appear (and flow into fastp).

So with workflow outputs we are now capturing everything from sample_fastq and that's why we see more files in the snapshot. Changing (basically, improving) the module to separate between input fastq, output fastq and undetermined will also change this snapshot (all the undetermined fastp results will also dissapear), so, in order for the changes not to be so big, I would merge this as-is and then do a whole refactoring of the sgdemux module and the outputs that are then captured in the workflow.

[atrigila]

Tracked here: #380

[apeltzer]

Fully agree on that approach 👍🏻

[apeltzer]

Looks good to me, follow up issues are tracked accordingly, nice :-)