6
23%
master: 23%

Ran 28 Mar 2018 06:59PM UTC

Files 39

Run time 1s

Badge

Committed 28 Mar 2018 06:40PM UTC coverage: 33.52% (-0.4%) from 33.88%

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

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)

Run Details

1979 of 5904 relevant lines covered (33.52%)

0.34 hits per line

Source Files on job 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])

broadinstitute / viral-ngs / 5816 / 6
23%
master: 23%

README BADGES
x

Markdown

Textile

RDoc

HTML

Rst

broadinstitute / viral-ngs / 5816 / 6 23% master: 23%

README BADGES x

Markdown

Textile

RDoc

HTML

Rst

broadinstitute / viral-ngs / 5816 / 6
23%
master: 23%

README BADGES
x