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Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.
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create pipeline for yale data #103

Closed Kurt-Hetrick closed 4 years ago

Kurt-Hetrick commented 4 years ago

they don't have any restrictions on their delimeter use so you can't apply any logic to parse out their file names as any array that you create will be of variable length and they use illumina to create their fastq files...so yeah, have to figure something out.

Kurt-Hetrick commented 4 years ago

so it looks like they created fastq files by tile, but again there is no logic, sometimes there are 10 files, sometimes there are 15 sometimes 16...so i am going to concatenate all of their tile files into one file...so that means that i can make everything 3 elements, but i will have to add something to handle they way illumina names their fastq files.

Kurt-Hetrick commented 4 years ago

modified pipeline to ingest the fastq files that I concatenated.