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CCBR / Pipeliner

An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
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miRseq pipeline #470

Closed shaoli86 closed 2 years ago

shaoli86 commented 2 years ago

I have an mirseq data which I am trying to run with ccbrpipeliner miseq pipeline. I have followed the instructions as outlined in the pipeliner documentation: https://ccbr.github.io/pipeliner-docs/miRNA-seq/TLDR-miRNASeq/#run-the-mirseq-pipeline However, when I am trying to dry-run the pipeline I am encountering this error:

KeyError in line 304 of {my_working_dir}/Snakefile: 'BOWTIE_REF' File "{my_working_dir}/Snakefile", line 304, in

skchronicles commented 2 years ago

Hey @shaoli86,

Do you remember what reference genome you selected from the drop down option? I am just wondering if you may have selected a reference genome that is not supported by this pipeline.

I have also emailed you about setting up a very quick meeting. It shouldn't take more than 15 minutes of your time. Please let me know what you think.

Best, @skchronicles

shaoli86 commented 2 years ago

Hi Skyler, I have chosen hg19 from the drop down list.

On Mon, Jan 24, 2022 at 10:58 AM Skyler Kuhn @.***> wrote:

Hey @shaoli86 https://github.com/shaoli86,

Do you remember what reference genome you selected from the drop down option? I am just wondering if you may have selected a reference genome that is not supported by this pipeline.

I have also emailed you about setting up a very quick meeting. It shouldn't take more than 15 minutes of your time. Please let me know what you think.

Best, @skchronicles https://github.com/skchronicles

— Reply to this email directly, view it on GitHub https://github.com/CCBR/Pipeliner/issues/470#issuecomment-1020253143, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEE65LQGILQMYXBA52KN4FDUXVZMBANCNFSM5MNJMNKA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

skchronicles commented 2 years ago

Hello @shaoli86,

Thank you for quickly meeting with us.

Yes, it appears the issue was due to selecting that (hg19) reference genome. At the current moment, the miR-seq pipeline only supports hg38 and mm10. @wong-nw and I will work together to add a warning message if a user selects an unsupported genome. This will help prevent the issue for others using the miR-seq pipeline.

Thank you again for bringing this issue to our attention, and have a wonderful day!

Best, @skchronicles

skchronicles commented 2 years ago

Note: Issue resolved with the following commit https://github.com/CCBR/Pipeliner/commit/e418e9f3aa11482d0c7d17999038418f134646e1.