Currently, we can't implement fastq.gz for an intermediate file b/c bowtie2 does not properly quote paths for --un-gz when it pipes to gz resulting in directories and input paths with spaces crashing.
All that needs to be done once spaces can be used in these paths is to change stage1_unmapped_reads_fastq_file_name to end in *.gz and to change the --un option to --un-gz. (Also, must enforce new minimum bowtie2 version.)
This currently works fine for paths that do not have spaces. Good catch, consistency test.
Currently, we can't implement fastq.gz for an intermediate file b/c bowtie2 does not properly quote paths for
--un-gzwhen it pipes togzresulting in directories and input paths with spaces crashing.All that needs to be done once spaces can be used in these paths is to change
stage1_unmapped_reads_fastq_file_nameto end in*.gzand to change the--unoption to--un-gz. (Also, must enforce new minimum bowtie2 version.)This currently works fine for paths that do not have spaces. Good catch, consistency test.