Update bowtie2 to use PE collection in ATAC-Seq data analysis tutorial #6542
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tflowers15
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heylf,
joachimwolff and
lldelisle
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@shiltemann and @bernt-matthias , I have updated the workflow and created a workflow tests file. As there was no exisiting workflow tests, could you please check I have created it correctly? I also added a test-data directory with the bed file that is created in the tutorial by querying the UCSC database. I know that best practice is to store the input datasets on Zenodo, but this file fairly small (72KB). |
shiltemann
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Dec 18, 2025
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thanks a lot @tflowers15! |
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Based on the GTN issue "Update tutorials to use collections instead of separate paired datasets #6377".
This update to the ATAC-Seq data analysis tutorial updates the version of bowtie2 used to 2.5.4+galaxy0 and replaces the separate paired end dataset inputs with a paired end collection (required PE input for this version of bowtie2). Also added the tool tip for creating paired end collections to the "Hands-on: Data upload".