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Enhancement: Update Kallisto wrapper adding option to save stdout as a dataset for MultiQC use #6610

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jennaj opened this issue Dec 4, 2024 · 0 comments

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@jennaj
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jennaj commented Dec 4, 2024

toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1

MultiQC will parse the stdout from Kallisto (only). The Galaxy wrapper for MultiQC seems ready to do this, but the file from Kallisto is not yet available. This request is to add an option to the Kallisto tool form to write that log as a dataset in the history for use in a workflow.

Xref

Where the log is in the stdout

Screen Shot 2024-12-04 at 12 53 02 PM

We could do something similar to how HISAT2's summaries in the stderr can be output to a log output.
Screen Shot 2024-12-04 at 1 13 55 PM

Alternatively: It would be super interesting to write a completely new tool that captures and writes out the stderr and/or stdout and/or info and/or description content -- from any dataset -- into the history as separate txt files. Maybe include a "stats" output with a checksum, timestamps, server/cluster details, anything else easily captured out of the technical metadata. Multi-use, we don't even need to know or care why. This probably needs a different ticket if anyone else likes the idea.

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