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genome-nexus / genome-nexus-annotation-pipeline

Library and tool for annotating MAF files using Genome Nexus Webserver API
MIT License
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PCM1 DNP annotation issue #156

Closed inodb closed 3 years ago

inodb commented 3 years ago

I've added several test cases in this PR. The main issue that this addresses is that Tumor_Seq_Allele1 wouldn't be updated when the reference allele was changed, even though in the input the mutations were identical.

Basically this:

8   17796381    17796383    AAC AAC AGT

became this after annotating

8   17796382    17796383    AC  AAC GT

Now it's fixed to output:

8   17796382    17796383    AC  AC  GT

I do have my doubts about changing/normalizing the mutations in general. It would be better to treat chrom,start,end,ref,alt as immutable imo. We've had multiple issues related to this, so maybe we should turn this off completely? If it's essential for particular studies, maybe we can opt-in with some command line flag (EDIT: filed an issue https://github.com/genome-nexus/genome-nexus-annotation-pipeline/issues/157)

ao508 commented 3 years ago

@sheridancbio @mandawilson @averyniceday Jenkins isn't able to run this workflow properly. I think I've narrowed down the issue to the script that checks for whether the owner of the PR is a trusted user or not.

I ran the script manually as the jenkins user and this is the response I got 

{u'documentation_url': u'https://docs.github.com/articles/creating-a-personal-access-token-for-the-command-line', u'message': u"Bad credentials. The API can't be accessed using username/password authentication. Please create a personal access token to access this endpoint: http://github.com/settings/tokens"}

I see a token had already been generated for the jenkins user but I think we need to update this check-pr-from-trusted-users.sh script to use the token instead of its git credentials file.

Would one of you be able to assist with this?

sheridancbio commented 3 years ago

@ao508 @inodb we are still working on the block for the jenkins tests, but we bypassed the check temporarily and the rest of the jenkins job ran to completion (successfully).