From d64b0ad1d18ab80adc486c4366206e72d8e99fec Mon Sep 17 00:00:00 2001
From: cgpu <38183826+cgpu@users.noreply.github.com>
Date: Thu, 12 Dec 2019 13:10:59 +0000
Subject: [PATCH] Updates resources, adds debug flags (#3)

* Removes residue bwaIndex from GRCh38

* Removes GenomeChronicler .dict, .fa.fai

* Testing 2FA

* Update nextflow.config

* Adds explicit memory definition for processes

* Adds more resources to BaseRecalibratorSpark processes

* Adds less resources to BaseRecalibratorSpark processes

* Adds ultra many resources; To revert back after test

* Restricts resources; Needed for using instances with Mem.GB/vCPU ratio equal to 4

* Update resources for PGP-UK

* Addresses https://github.com/cgpu/sarek/issues/3 ; Known issue with bwa | smatools pipe

* Updates resource alloc to *Spark versions; Adds retry for MultiQC

* Adds new image built with https://github.com/PGP-UK/GenomeChronicler/commit/5513c6f7d61952615d4a148f4df9ff90aa2de25d

* Adds verbosity INFO for debugging

* Freezes broadinstitute/gatk to 4.1.4.0

* Change GATK Spark tools verbosity to debug

* Restricts resource alloc of MarkDuplicatesSpark

* Removes explicit resource alloc from bamqc (qualimap)

* Removes metrics file; Refer to this: https://gatkforums.broadinstitute.org/gatk/discussion/23441/markduplicatespark-is-slower-than-normal-markduplicates

* Downgrades gatk from 4.1.4.0 to 4.1.3.0

* Returns mapping to nfcore version 2.5.1