New module: custom/splitfastqbylane

[anoronh4]

This is a custom module using awk to split a single fastq or fastq pair into multiple fastqs or fastq pairs, where each comes from a single lane+flowcell source. This is for when the raw data input is merged. This tool uses an awk statement to read the input file and direct the output to different files based on the content of the fastq header.

PR checklist

Closes #2836

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[SPPearce]

Is this module still useful?

[anoronh4]

Is this module still useful?

In my and my colleague's opinion yes. We still have previously merged fastq files that come our way, and for base quality recalibration purposes, we align them separately so that each read gets a read-group label based on the flowcell/lane it came from. i asked for feedback on this module some time ago.

[SPPearce]

Yes, I see that nobody reviewed the module 😔.
If you are still interested, we can get it finished off and merged in.
It will need swapping to nf-test, but I can help with that.

[adamrtalbot]

Is this module still useful?

In my and my colleague's opinion yes. We still have previously merged fastq files that come our way, and for base quality recalibration purposes, we align them separately so that each read gets a read-group label based on the flowcell/lane it came from. i asked for feedback on this module some time ago.

BQSR will read the lane tag in the BAM file, assuming you're using it correctly.

Other than that the code looks fine but we should update to nf-test now.

[SPPearce]

So shall we swap this to nf-test and merge it in?