Accommodate bulk fastq files without `R1` in the file name about scpca-nf HOT 5 CLOSED

I wonder if we can use glob negation for R1 files:

Something like:
"!(*_R2_*).fastq.gz"

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To expand a bit: R1 or untagged fastq files should be caught would be caught by "!(*_R2*).fastq.gz" and R2 files would still be caught by "*_R2*.fastq.gz". But I just realized this won't work in the case that there are I1 files in the directories, which we definitely have.

I actually think I might favor adding _R1_ to the file names in cases like this, rather than making the workflow more complex

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I actually think I might favor adding R1 to the file names in cases like this, rather than making the workflow more complex

I'm fine with this if that's what we want to do. The only thing it means is that if we get additional bulk files that have no R1 like these, then we will have to do the same thing and remember to rename them.

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I actually think I might favor adding R1 to the file names in cases like this, rather than making the workflow more complex

I'm fine with this if that's what we want to do. The only thing it means is that if we get additional bulk files that have no R1 like these, then we will have to do the same thing and remember to rename them.

Agreed... it's a bit messy, but since we do enforce filenames otherwise, I think we should be okay. We will also need to make sure to update the md5 files to match.

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Agreed... it's a bit messy, but since we do enforce filenames otherwise, I think we should be okay. We will also need to make sure to update the md5 files to match.

Okay, I'm going to close this and file another issue in ScPCA-admin to track changing the filenames and md5s.

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