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broadinstitute / viral-ngs / 5816
23%

Build:
DEFAULT BRANCH: master
Ran 28 Mar 2018 06:59PM UTC
Jobs 2
Files 45
Run time 6min
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kraken summary parser (#792)

* add kraken summary parser to process multiple reports and return some basic aggregations in csv and json format

* conditional json output

* add zero fill option to kraken parser, allow no_hist regardless of top taxa count

* refactor for readability

* additional help text for taxlevel_summary

* add --includeRoot to taxlevel_summary

--includeRoot includes the root-level and unclassified read counts.
Also change the defaults for taxlevel_summary (focus on species, 100
most abundant taxa with >1 read each)

116 of 116 new or added lines in 1 file covered. (100.0%)

6174 of 8766 relevant lines covered (70.43%)

0.93 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
98
100.0
metagenomics.py
Jobs
ID Job ID Ran Files Coverage
5 5816.5 (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]) 28 Mar 2018 07:06PM UTC 0
70.37
Travis Job 5816.5
6 5816.6 (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]) 28 Mar 2018 06:59PM UTC 0
33.52
Travis Job 5816.6
Source Files on build 5816
Detailed source file information is not available for this build.
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