I am running the Picard tool CollectSequencingArtifactMetrics in galaxy (locally in my pc).
The output files are saved into disk and not passed to stdout and (I guess) they can't be passed as output from picad to galaxy .
In the xml file I am including:
<outputs> <data name='preSummary' format="tabular" from_work_dir="pref.pre_adapter_summary_metrics"/> </outputs>
When I click on View details, in "stderr", I see:
[Mon Mar 11 13:43:07 EDT 2019] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.19 minutes. Runtime.totalMemory()=3323461632
1 - It looks like it worked but shouldn't I see the highlighted information in "stdout" rather than in the "stderr"?
2- If it worked, How can I get my output files? I tracked the working directory printing
pwd from the
<command> but I guess all files are deleted immediately once the picard process has finished.
Any idea of what am I doing wrong?
What basic knowledge am I missing here?