Looking for MultiQC report in the wrong place?

eastgenomics / eggd_artemis

Creates download urls for files required and outpus in a text file to be shared with the scientists

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Looking for MultiQC report in the wrong place? #22

Open chrispyatt opened 2 months ago

chrispyatt commented 2 months ago

See job: https://platform.dnanexus.com/panx/projects/GgJ3gf04F80JY20Gjkp0QjF4/monitor/job/GjPykg84F80BB23Fx1gJ8Bgv

Logs contain the line below: No MultiQC report given, searching instead with path /output/CEN-240226_1342/dias_reports_v2.2.1_SNV/240417_1537

But the MultiQC report isn't in the dias_reports directory. It's in /output/CEN-240226_1342/eggd_MultiQC/

rklocke commented 2 months ago

It only uses this path to find MultiQC reports which begin with the same single path, i.e. /output/CEN-240226_1342: https://github.com/eastgenomics/eggd_artemis/blob/main/src/eggd_artemis.py#L421-L423

But the logs could definitely be clearer.. The issue for this job seems to be that the original MultiQC report in this project was deleted so it is trying to make a download link for a file which doesn't exist - this should be fixed (though in the meantime giving the MultiQC report as an input will work)