nmdp-bioinformatics / pipeline

Consensus assembly and allele interpretation pipeline.
GNU Lesser General Public License v3.0
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splitter gives non-intuitive message when handed only compressed fastq files #29

Closed janders3-nmdp closed 9 years ago

janders3-nmdp commented 9 years ago

Another check should be added so that if it finds only fastq.gz files, it warns that said files need to be gunzip'd. Or, perhaps it could try to gunzip them itself?

janders3-nmdp commented 9 years ago

77 might be considered to fix this, as the regex is smarter now, and will exempt any file ending in .gz or .bz2

janders3-nmdp commented 9 years ago

77 now prevents splitter from running when handed only compressed .fastq or .fq files.

This isn't a perfect-world fix, but does follow the letter of fixing issue #29.