STAR unmapped reads not output

[ameynert]

Suggest change in process star - this will output files of format Unmapped_R{1,2}.fastq.gz to the unmapped folder.

else if (params.saveUnaligned && filename != "where_are_my_files.txt" && (filename =~ /Unmapped/)) "unmapped/$filename".replaceAll(/\.out\.mate(\d)/, '_R$1.fastq')

And this at the end of the process:

          if [ $params.saveUnaligned ]
          then
            gzip *Unmapped*
          fi

[drpatelh]

I have added some logic in the STAR DSL2 module here that will check if the unmapped files exist and if so, to rename and zip them. The logic to publish has changed too for DSL2 so the snippet below should achieve this if -save_unmapped is speficied:

if (params.save_unaligned)       { params.modules['star_align'].publish_files.put('fastq.gz','unmapped') }