6535
23%

Ran 27 Jul 2018 09:03PM UTC

Jobs 2

Files 41

Run time 8min

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Build # 6535

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

demux changes to support novaseq (#868)

* reduce demux memory footprint to 80% of system max

* remove force_gc=false default from viral-ngs

remove force_gc=false default from viral-ngs, as force_gc=true is now the default in Picard: https://broadinstitute.github.io/picard/command-line-overview.html#IlluminaBasecallsToSam

* maxReadsInRamPerTile, maxRecordsInRam, and forceGC in demux WDL workflow

* memory to 85%

* autoscale some novoseq demux params, allowing override by passed-in param values

* tune -Xmx memory limit for Novaseq demux

* max_mismatches 0 -> 1; minimum_base_quality 25 -> 10

max_mismatches 0 -> 1; minimum_base_quality 25 -> 10

Run Details

1 of 1 new or added line in 1 file covered. (100.0%)

2050 of 6349 relevant lines covered (32.29%)

1.03 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
5	6535.5 (TRAVIS_JOB=test_py36 PYTEST_ADDOPTS="-rsxX -n 2 --durations=25 --fixture-durations=10 --junit-xml=pytest.xml --cov-report= --cov broad_utils --cov illumina --cov assembly --cov interhost --cov intrahost --cov metagenomics --cov ncbi --cov read_utils --cov reports --cov taxon_filter --cov tools --cov util --cov file_utils")	27 Jul 2018 09:11PM UTC	0	72.98	Travis Job 6535.5
6	6535.6 (TRAVIS_JOB=test_snakemake PYTEST_ADDOPTS="-rsxX -n 2 --durations=25 --fixture-durations=10 --junit-xml=pytest.xml --cov-report= --cov broad_utils --cov illumina --cov assembly --cov interhost --cov intrahost --cov metagenomics --cov ncbi --cov read_utils --cov reports --cov taxon_filter --cov tools --cov util --cov file_utils")	27 Jul 2018 09:03PM UTC	0	32.29	Travis Job 6535.6

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