enabled storeDir for dsl2

[anoronh4]

Addresses #1000 . Very similar to #1001 but for the dsl2 version of the pipeline, and merging to the develop branch, rather than for the dsl1 version and merging directly to master.

Currently only the alignment_wf has been adjusted, and no config file for enabling storeDir has been added to the branch. Suggested config usage for now is:

process {
    withName: 'alignment_wf:.*' {
        storeDir = { "storeDir/${task.process}/${task.tag}/" }
    }
}

and specifying the file to nextflow using -c my_config

[johnoooh]

Looks good.