wochenende alignment fails if nodup not set up - duplicates

[colindaven]

• .dup.bam is a required output by nextflow at present
• but we allow the dup removal as an option
• however, .dup.bam required later too (plots etc)
• perhaps make standard on, but useful info available from files containing dups
• Actually related to long reads, where dup removal is off by default (has little or no impact since uses identical start positions to find dups, unlikely for long reads)

Error executing process > 'wochenende (20220726_organelle_ont_R1.fastq)'

Caused by:
  Missing output file(s) `*.dup.bam` expected by process `wochenende (20220726_organelle_ont_R1.fastq)`