6
23%
master: 23%

Ran 25 Jan 2018 10:51PM UTC

Files 39

Run time 2s

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Committed 25 Jan 2018 10:16PM UTC coverage: 33.749%. Remained the same

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

tomkinsc

Commit Message

fixes to align_and_plot workflow (#766)

* change default align_and_plot.wdl workflow to use loose novoalign params, change both plot_coverage invocations to: not fail when mean_coverage is < 1, not fail when reads_aligned=0 (ie, output zero byte coverage plots and fastqc reports)

* run reports.py fastqc always, since its smart enough to defend against zero input

Run Details

1948 of 5772 relevant lines covered (33.75%)

0.34 hits per line

Source Files on job 5421.6 (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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