If non-gzipped files are given, they are copied to a location where they have the .gz extension. This confuses fastqc and it crashes.
Our solution was to gzip the input the files in place and re-run, but yeat probably shouldn't do that. My preferred solution would be to copy the files with the .gz extension only if they are gzipped to start. When the reads get to fastp, sending the filtered reads to an output with the .gz extension will trigger compression, so no rules using the filtered reads as input would have to change.
If non-gzipped files are given, they are copied to a location where they have the
.gzextension. This confusesfastqcand it crashes.Our solution was to gzip the input the files in place and re-run, but
yeatprobably shouldn't do that. My preferred solution would be to copy the files with the.gzextension only if they are gzipped to start. When the reads get tofastp, sending the filtered reads to an output with the.gzextension will trigger compression, so no rules using the filtered reads as input would have to change.