amplicon_sorter doesn't find demultiplexed reads #3
Description
Dear AmpliPiper Team,
when running your pipeline I encountered the issue that amplicon_sorter was not able to find the demultiplexed data.
I think the issue is located in this code section: AmpliPiper.sh L428-456. To my understanding, the issue is that AmpliPiper tries to access the file defined as ${output}/data/demultiplexed/${samplename}/${primername}.fastq \ in Line 449. However, it already changed into the directory ${output}/data/demultiplexed/${samplename}/ in Line 430. Removing this line fixed the amplicon_sorter step for me, but I'm not entirely sure about the consequences further downstream.
Best whishes
Yannis Schöneberg