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mpc-bioinformatics / McQuaC

Transform the Quality Control workflow from Knime into a workflow in Nextflow
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fix error when procesing non ISA files #49

Closed di-hardt closed 5 months ago

di-hardt commented 6 months ago

Running the workflow with --main_is_isa false returned error Access to 'retrieve_spikeins.out' is undefined since the workflow 'retrieve_spikeins' has not been invoked before accessing the output attribute as retrieve_spikeins is only executed with --main_is_isa true.
I added a simple if-statement to get around this issue but the spike in colums are missing in the quality_control.csv. Does it introduce any issue in the future for the analysis or visualization?
It is not ideal for the databse insertion but not a real drama.

KarinSchork commented 6 months ago

These spike-in columns are not visualized so this should not lead to a problem in the QC_visualization script.

KarinSchork commented 6 months ago

but maybe we want to have them in the filtered "human-readable" version of the table that is also shown in nf-cloud?

di-hardt commented 6 months ago

Makes sense but it needs to be optional then.

di-hardt commented 6 months ago

This issue is also a bit related to this PR: https://github.com/mpc-bioinformatics/Next-QC-Flow/issues/50

KarinSchork commented 6 months ago

Yes. I think there is still a (currently unused) isa flag in the visualization script, I could try to use that.