additional test in check_data_integrity.py

caporaso-lab / mockrobiota

A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.

http://mockrobiota.caporasolab.us

BSD 3-Clause "New" or "Revised" License

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additional test in check_data_integrity.py #41

Open gregcaporaso opened 7 years ago

gregcaporaso commented 7 years ago

Should check that linked files have:

one of the following names: mock-forward-read.fastq.[gz|zip], mock-reverse-read.fastq.[gz|zip], mock-index-read.fastq.[gz|zip]
no duplicated names
links exist for forward and index files (reverse is optional)

nbokulich commented 7 years ago

Also: automatically check validity of raw data, e.g., confirm that files are readable and (possibly) in valid fastq format (issue with the latter is that, depending on the software we use and the age of the dataset, header lines that are valid fastq may not be recognized by the software)