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Bug fix: update version of BWA-MEM in Hi-C workflow to avoid fatal index error #5278

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jennaj opened this issue Sep 3, 2024 · 1 comment

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bug help-wanted

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jennaj commented Sep 3, 2024

Ref workflow: https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/hicexplorer/workflows/
Ref IDC feedback: galaxyproject/idc#53
Ref reported at https://help.galaxyproject.org/t/convert-galaxy-output-hic-file-to-hic-file-for-use-on-ucsc-genome-browser/12833/4

Workflow fails at BWA-MEM step when accessing dm3 index.

Workaround for end-users

Load the workflow into Galaxy

Open the workflow in the Editor

Update BWA-MEM to the latest tool version

Save, then execute

jennaj added the bug label

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jennaj commented Sep 3, 2024

Test at EU

Note: the hands-on could be updated for this, too (uses an older version of Bowtie)

hexylena added the help-wanted label

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