Remove storeDir semantic structure

[nebfield]

Although we were only using stored files as a permanent cache and not publishing them, we were organising outputs into a semantic structure, e.g.:

storeDir $workDir/${meta.id}/${meta.chrom}

From nextflow docs:

The storeDir directive is meant for long-term process caching and should not be used to publish output files or organize outputs into a semantic directory structure. In those cases, use the publishDir directive instead.

As a side effect this also broke cloud executors in subtle ways.

Now flat directories are used and processes have been updated to correctly capture output file names, instead of using wildcards.

[smlmbrt]

Makes sense to me