Awsbatch modifications

[maxulysse]

• 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

[maxulysse]

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

[maxulysse]

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

[maxulysse]

@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.

[alneberg]

Looks nice!