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Awsbatch modifications#679

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alneberg merged 9 commits intoSciLifeLab:devfrom
maxulysse:awsbatch
Nov 2, 2018
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Awsbatch modifications#679
alneberg merged 9 commits intoSciLifeLab:devfrom
maxulysse:awsbatch

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@maxulysse maxulysse commented Nov 1, 2018 •
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  • change path for genome_base
  • change queue for awsbatch
  • add container for CreateIntervalBeds
  • add publishDirMode for germlineVC.nf

PR checklist

  • PR is made against dev branch
  • This comment contains a description of changes (with reason)
  • Ensure the test suite passes (./scripts/test.sh -p docker -t ALL).
  • CHANGELOG.md is updated

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maxulysse commented Nov 1, 2018

@apeltzer Sorry, I noticed that I forgot some PublishDir mode link in the germlineVC.nf script

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maxulysse commented Nov 1, 2018 •
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EDIT: that was obviously meant for @alneberg sorry everyone about the mention

@alneberg when all the files are uploaded to the s3 bucket, you can make a file relating to that there:
https://github.com/SciLifeLab/Sarek-data/tree/master/testdata/tsv
and then update the submodules on Sarek

We still need to sort out this s3 bucket results issue

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maxulysse commented Nov 2, 2018

@alneberg I added the path to this temporary s3 bucket genome.
Remember to use iGRCh38 for the genome

At the same time I removed COSMIC files as it was no longer used.

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alneberg approved these changes Nov 2, 2018
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Looks nice!

@alneberg alneberg merged commit e53b2ba into SciLifeLab:dev Nov 2, 2018
This was referenced Jan 31, 2019
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