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LieberInstitute / BiocMAP

Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow
http://research.libd.org/BiocMAP/
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Untrimmed uncompressed FASTQ files are published as outputs #14

Closed Nick-Eagles closed 1 year ago

Nick-Eagles commented 3 years ago

This is a minor issue, but can potentially waste a fair bit of disk space. If trimming settings are such that not all samples are trimmed, any untrimmed samples beginning as compressed FASTQ files are decompressed (necessary for Arioc) and these decompressed FASTQs are published to the output folder in the Trimming subdirectory. Decompressed FASTQs are temporary files and should not be included as outputs.

Nick-Eagles commented 3 years ago

Clarification: ALL untrimmed FASTQs are published as output files, which is even worse. Files should only be published as outputs when a given sample is trimmed.