Add demultiplexing step about ampliseq HOT 7 OPEN

What about adding a few optional columns (such as fw_index, rv_index) to the sample sheet. If those columns are present, demultiplexing will run. If that might mess too much with existing routines, a separate input file (e.g. --demultiplex "sheet.tsv") that contains the necessary information (samplesheet & demultiplexsheet have identical IDs) might be an option?
While ampliseq does not require a samplesheet (folder input & fasta input are also allowed), for demultiplexing that would be fine. After all, a samplesheet can handle more info than a folder input. Not all input options need to support all functionality, imho.

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This might be a helpful feature. As far as I know there is work ongoing for wrapping DADA2 directely in this pipeline instead of QIIME2 using DADA2. Therefore I am unsure how to integrate this feature sustainably with the major changes that are planned to the early workflow. However, PRs are welcome.

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@DiegoBrambilla is planning to implement dada2 for PacBio analysis and could immediately add that demultiplexing step :)

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We take it into consideration.
For the time being, implementing the R-DADA2 pipeline, taxonomy annotation from several sources and dealing with PacBio reads take priority.

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Demultiplexing could be done via cutadapt as documented here. I never come across the need for demultiplexing in the pipeline, but if anyone does, please mention it here and I might further look into it.

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I want to add demultiplexing (with Cutadapt) to Ampliseq. The way I've handled demultiplexing in my own nf-core style pipeline is to ask the user to specify the path to their raw data in the command line --raw_data "/path/to/data/*{R1,R2}*.fastq.gz". Then in the sample sheet the user has to add the columns fw_index, rv_index, fw_primer, and rv_primer (the two rv_ columns can be empty for single-end data). I use the _index columns for demultiplexing and the _primer columns for trimming after demultiplexing. The main issue I see is that Ampliseq doesn't require a sample sheet as input, so I'm wondering if anyone has a suggestion for a better way of adding this feature to Ampliseq? Maybe the sample sheet should be required if the user wants to demultiplex?

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To me, adding columns to the sample sheet sounds best.

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