Thank you for your hard work on this tool! I was recently debugging an issue where trimmomatic seemed unable to cut standard Illumina adapters that I wanted to bring to your attention. After some extensive investigation, I realized I was selecting a non-existent adapter file as the source of sequences to scan against the read data. No error was reported by Trimmomatic, so I'm guessing that adapter trimming was just skipped as a result.
Would it be possible to exit with an error code if the adapter file is missing? I know this is only the case with custom adapters, but may be a useful condition to prevent for other users.
Hi,
Thank you for your hard work on this tool! I was recently debugging an issue where trimmomatic seemed unable to cut standard Illumina adapters that I wanted to bring to your attention. After some extensive investigation, I realized I was selecting a non-existent adapter file as the source of sequences to scan against the read data. No error was reported by Trimmomatic, so I'm guessing that adapter trimming was just skipped as a result.
Would it be possible to exit with an error code if the adapter file is missing? I know this is only the case with custom adapters, but may be a useful condition to prevent for other users.