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Question: MultiQC and collections
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gravatar for d.hand
4 weeks ago by
d.hand • 0
d.hand • 0 wrote:

Is anyone experienced with MultiQC and element identifiers for collections? I'm currently using the custom content option, but it doesn't name the samples correctly, unlike the output of bowtie,fastp ect. Has anyone found a way around this?

It would be nice to extract the elements of the list and supply them to the tool, but i take it we are not able todo this with collections.
collections multiqc • 64 views
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modified 26 days ago by Jennifer Hillman Jackson ♦ 25k • written 4 weeks ago by d.hand • 0
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gravatar for Jennifer Hillman Jackson
26 days ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Collection datasets can be individually dragged and dropped into tool forms as inputs. That might be enough for your purposes?

Also please see the tools in the group: Collection Operations. In particular, these:

  • Relabel List Identifiers from contents of a file
  • Filter List from contents of a file
  • Apply Rule to Collection

Tutorials: https://galaxyproject.org/learn/

If you think MultiQC has a bug with respect to reading in the collection element identifiers and reporting those in the report, please create an issue at https://github.com/galaxyproject/tools-iuc/issues. If you want to vet it first (best), contact the IUC tool authors at their Gitter chat here: https://gitter.im/galaxy-iuc/iuc. This functionality is still somewhat new and not all tool wrappers use this specific collection information yet as far as I know. Running the analysis using an older version of Galaxy could be a factor, too. Upgrade to release 18.09 if running this at your own local to see if that fixes the problem. Make certain that the most current version of MultiQC and the upstream tool that generated the report given to MultiQC are installed and/or used.

When discussing the problem with the authors, including an example such as a shared history link showing the behavior (if possible) might be requested. Be prepared to note which tool versions you are using, where the analysis was done (if a public Galaxy, by URL), and the version of Galaxy (if running at your own local).

Thanks! Jen, Galaxy team
ADD COMMENT • link written 26 days ago by Jennifer Hillman Jackson ♦ 25k
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