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sanjaynagi / AmpSeeker

A snakemake workflow for amplicon sequencing
https://sanjaynagi.github.io/AmpSeeker/
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Fix for childioexception error #70

Closed ChabbyTMD closed 1 year ago

ChabbyTMD commented 1 year ago

Addresses #69 Use a holding directory in resources for reads generated from bcl_convert. Reads are subsequently renamed and moved to reads dir for usual workflow execution.

sanjaynagi commented 1 year ago

Did you still get this error when updating snakemake @ChabbyTMD ?

ChabbyTMD commented 1 year ago

Hi Sanjay, can I follow up on this later this evening. I've been having issues updating my snakemake install on my cluster workspace.

sanjaynagi commented 1 year ago

No worries Trevor. If it is the snakemake version, we should merge anyway, as it’s better for the workflow to work with diff versions of snakemake Sent from my iPhoneOn 14 Jul 2023, at 14:44, Trevor Mugoya @.***> wrote: Hi Sanjay, can I follow up on this later this evening. I've been having issues updating my snakemake install on my cluster workspace.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: @.***>

ChabbyTMD commented 1 year ago

Hi Sanjay, I receive the same error while using snakemake 7.30.1. Also, I have a fix for the missing fastp and qualimap outputs in multiqc. Will add this to a separate PR.

sanjaynagi commented 1 year ago

Ok, going to merge this now. Thanks Trevor.

Hopefully it doesn't cause issues with the other PR, that one might need updating, not sure :)