in preprocessing/preprocessing.snakefile, line 17, the extensions used are hardcoded. Shouldn't tuple(['fastq.gz', 'fq.gz']) be replaced with EXTENSION if this is going to be pulled from the config to begin with? I encountered this by providing some *.fq files, specifying '.fq' as my extension, and still getting no result until I made this substitution. Just making sure as I'm not too familiar with this code.
bsiranosian
commented
5 years ago
in preprocessing/preprocessing.snakefile, line 17, the extensions used are hardcoded. Shouldn't
tuple(['fastq.gz', 'fq.gz'])be replaced withEXTENSIONif this is going to be pulled from the config to begin with? I encountered this by providing some *.fq files, specifying '.fq' as my extension, and still getting no result until I made this substitution. Just making sure as I'm not too familiar with this code.