bwa mem | samtools sort hybrid command introduces inefficiency ( up to 3x longer runtime) #3
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* 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 cgpu#3 ; Known issue with bwa | smatools pipe * Updates resource alloc to *Spark versions; Adds retry for MultiQC * Adds new image built with PGP-UK/GenomeChronicler@5513c6f * 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
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Refactor this and sacrifice I/O inefficiency because the gain is larger by the fix of resource misalloc.
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