Can't add BAM files to Workflow: QC report (tutorial 1:RNA-Seq reads to counts)

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Hi all,

I’m following along the RNA-Seq reads to counts tutorial with my own data and am up to the Generating a QC Summary Report step.
I’ve followed the instructions (imported the QC report workflow, downloaded the RefSeq BED file) but in the workflow I cannot seem to select my BAM files - it only gives me the option to select MultiQC files.

Any help would be appreciated! Thanks

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It is a bit hard to debug for me so I hope someone else can give a better answer . But if I go to the workflow page after getting the workflow I see this:

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image1292×123 4.88 KB

And after I click “run workflow” I see this:
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image1309×292 11.1 KB

Do you see the same? Did you used the url to import the workflow?

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Hi, thanks for your reply

Yes I see the same there, however my issue is I can’t select any BAM files to enter, it will only let me chose MultiQC files in the drop-down menu

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image1323×414 22.4 KB

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Hi - are you still having this problem?

If so, some items to check:

  1. The BAM inputs should be in a dataset collection.
  2. That collection needs to be in the same history where the workflow is launched (the “active” history).
  3. And, this workflow is run after the completion of the other workflow associated with this tutorial.

If you want to share a link to your tutorial history back, we can help to test more. FAQ sharing-your-history

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