Handle single fastq files as inputs about flowcraft HOT 8 OPEN

I agree that this will be a good thing to support. From the point of view of assemblerflow, the required modification is trivial. The fromFilePairs channel could be defined as:

Channel.fromFilePairs(params.reads, size: params.singleEnd ? 1 : 2, type: 'file')

To allow for both single and paired-end data. However, the majority of the modifications would be on the template scripts themselves, which are mostly designed for paired end data. Moreover, we would need to create a requirement that templates using fastq data would need to support from single and paired-end files, whenever possible.

When that isn't a possibility, that should be explicit in the documentation of the component using the template (and perhaps including a check in pipelines using those components that prevent the input of single end data.

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Also a statement like this can be used in each process template that requires to handle both paired end or single end inputs.

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Yes, my point is precisely that we can leave that handler to the process itself or to the python script as you say.

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I've been receiving request to support single FastQ files as input. @tiagofilipe12 example is no longer available but I like @ODiogoSilva solution of having both possibilities in each template. A simple solution is to duplicate the scripts and adjust accordingly.

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Double the scripts, double the maintenance effort. It seems easier to have the FastQ channel accepting both paired and single reads and then add a condition in the templates depending on the number of fastq received.

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I agree. I was just thinking about tools where you have to input each fastq file in a different parameter or that have completely different parameters depending if you're working with paired-end or single fastq files.

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Does Flowcraft support interleaved paired-end FASTQ file, for example as output by samtools mergepe? That's my preferred format, by far, for paired-end reads.
I opened issue #136 for this feature request.

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