6
23%
master: 23%

Ran 06 Jun 2018 06:45PM UTC

Files 39

Run time 4s

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Committed 06 Jun 2018 06:27PM UTC coverage: 33.283% (-0.2%) from 33.52%

Job # 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" BUNDLE_SECRET=[secure]

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

add read_utils.py downsample_bams (#819)

* add read_utils.py downsample_bams

* change arg expansion for py2

* add unit tests

* reduce JVMmemory used for unit tests of downsample_bams

* add simple read_utils wdl file

first function to be included is downsample_bams

* pass JVMmemory to rmdup_mvicuna_bam in downsample_bams

* add workflow for downsample_bams

* add input file to reads.wdl

* remove workflow aliasing

* rename workflow

* switch to ThreadPoolExecutor; pass through treads and JVMmemory more carefully

* decrease JVMmemory for downsample_bam wdl

* downsample workflow array input

* wdl conditional correction

* wdl readcount param correction

Run Details

1994 of 5991 relevant lines covered (33.28%)

0.33 hits per line

Source Files on job 5953.6 (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" BUNDLE_SECRET=[secure])

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