opened
mr-c
username_0
There should be a single and consistent file naming scheme and is user overridable.

Being able to specify the output file name is a requirement for building pipelines in iPlant's DiscoveryEnvironment.

Known offenders: 
load-graph.py appends a .ht to the filename specifed (???)

(Others as I find them again)
Inconsistent and incomplete output filename handling
issue
created
ctb
username_1
A few more thoughts here, to throw against the wall --

1. -o could override all other options, and be an aggregate of all output.

2. for multi-file input, we should stop building filenames like '.keep.abundfilt.foo.bar.baz' and start building filenames like '.keep.abundfilt.fq.gz' where we specify fq/gz.

3. -d (or something) could specify output _directory_ in case of the above; right now it is always '.', but could be overridable.

4. For FASTA/FASTQ, in general only one file should ever be output for each input. This means 'broken paired' format, I think.
comment