Output folder wrong
lczech opened this issue · 11 comments
Hi there!
The documentation states that
The results will directly be stored under the output folder specified with -o
See https://damageprofiler.readthedocs.io/en/latest/contents/generalUsage.html#how-to-run
However, when running DamageProfiler, instead, there is another directory created below the specified one, named after the input file without its sam/bam extension. I hope I didn't overlook a setting, but that is what I got.
I'd prefer if the tool actually behaved as documented, as this makes it easier to use in Snakemake and other pipeline tools.
Cheers and thanks
Lucas
Hi Lucas,
which version of DamageProfiler are you using? The documentation refers to version 1.0. The behaviour that you are describing was used in all versions before 1.0.
Thanks for pointing this out, I'll make it more clear in the docu.
I hope this clarifies your question.
Cheers,
Judith
Hi Judith,
thanks for the quick reply. I'm using the latest bioconda version, which is 0.5.0
Weird that 1.0 is not yet available there - doesn't that update automatically?
Cheers
Lucas
@JudithNeukamm should I wait for a point release with the fixed JSON output before bumping?
@jfy133 I'll release a fixed version 1.1 today.
Thanks all! Ah okay, I see. I've never set up a bioconda recipe myself - and from what I knew I assumed that bioconda detects new versions automatically. Thanks for the clarification, and thanks for the quick fix!
Thanks all! Ah okay, I see. I've never set up a bioconda recipe myself - and from what I knew I assumed that bioconda detects new versions automatically. Thanks for the clarification, and thanks for the quick fix!
There are varying levels of automation but this can be shaky.
@jfy133 Version 1.1 is released
Bioconda PR: bioconda/bioconda-recipes#24899 Hopefully straight forward!
bioconda/bioconda-recipes#24899 @lczech merged! Give it an hour or so and you'll hopefully be able to run aain with 1.1!
Thanks, that worked! :-)