Detected samplesheet adapters being passed through the pipeline to fastp for trimming

[edmundmiller]

It would be really interesting if we could pass the trimmed adapters from the samplesheet as args downstream to fastp.

Instead of what currently happens, the adapters are removed, and the pipeline relies on Fastp's defaults or requires users to specify the adapters in a config.

That would allow us to perform more specific trimming using FastP.

[grst]

At least for paired end data, fastp docs say there's no added value to specifying the adapters compared to autodetection:

For PE data, the adapters can be detected by per-read overlap analysis, which seeks for the overlap of each pair of reads. This method is robust and fast, so normally you don't have to input the adapter sequence even you know it.

And I'd rather rely on the autodetection than relying on someone not making a typo in the samplesheet. So I'm not convinced adapters should be taken from the samplesheet by default.

Relevant fastp docs section: https://github.com/OpenGene/fastp?tab=readme-ov-file#adapters

[ashotmarg]

Hi guys, thanks for getting the discussion going and @edmundmiller for creating this issue. This issue was created due to the errors we had when we were running not very-long amplicon sequences. Apparently, in our case, fastp mistakenly recognised a 60 bp sequence at the 5’ (i.e., beginning) of the reads (not 3’ as normally adapters are) as adapters and since these are at the 5’ ends and everything else after the adapters are removed, it effectively removed the whole reads. Unfortunately I cannot share the data, due to the potentially sensitive nature of the sequences, but we lost >90% of the data and will be happy to elaborate.

[edmundmiller]

Another interesting use case would be if a user just wanted the stats from fastp, but without trimming with fastp. They could trim with the demultiplexer or not at all.

demultiplex/conf/modules.config

Line 120 in 7c2040c

// if ! params.trim_fastq, only output reports but not trimmed fastq files