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broadinstitute / viral-ngs / 5953
23%

Build:
DEFAULT BRANCH: master
Ran 06 Jun 2018 06:45PM UTC
Jobs 2
Files 39
Run time 9min
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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

87 of 87 new or added lines in 1 file covered. (100.0%)

1994 of 5991 relevant lines covered (33.28%)

1.02 hits per line

Jobs
ID Job ID Ran Files Coverage
5 5953.5 (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" BUNDLE_SECRET=[secure]) 06 Jun 2018 06:54PM UTC 0
69.89
Travis Job 5953.5
6 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]) 06 Jun 2018 06:45PM UTC 0
33.28
Travis Job 5953.6
Source Files on build 5953
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