Troubleshooting

Setup problems

Please leave us an issue and we will try to help out.

If you get missing or 0 sized empty bams in output of wochenende

• Check most recent work folder
• cd work && ls -lrt
• Go into most recent folder and subfolder
• ls -l
• cat .command.err
• It could be that trimming adapter files or the program perldup have not been located correctly
• Check your config.yml that the locations to these tools are correct.
• Also check the aligner bwa is accessible within the wochenende conda environment. Type conda activate wochenende && bwa

Reference problems

If you want to use your own reference sequence, follow the guide on this Wiki at https://github.com/MHH-RCUG/nf_wochenende/wiki/Building-a-reference-sequence for best results. Contact us via issue if problems persist.