• Home
  • Features
  • Pricing
  • Docs
  • Announcements
  • Sign In

broadinstitute / viral-ngs / 1224
23%
master: 23%

Build:
Build:
LAST BUILD BRANCH: ct-krakenuniq-summary-kmer-filter
DEFAULT BRANCH: master
Ran 28 Mar 2020 12:06AM UTC
Jobs 2
Files 43
Run time 4min
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst

pending completion
1224

push

travis-ci-com

tomkinsc
Update read_utils.py

The old mvicuna post-processing code expects read IDs to have a /1 mate suffix, and only includes those that do, which single-end reads do not have (nor interleaved fastqs, but that's a separate issue and we're generating the fastqs for this internal function ourselves so interleaving should not be an issue). So no single-end IDs were preserved. This ensures single-end read IDs make it through this post-processing.

293 of 2691 branches covered (10.89%)

2 of 2 new or added lines in 1 file covered. (100.0%)

1452 of 6242 relevant lines covered (23.26%)

0.92 hits per line

Jobs
ID Job ID Ran Files Coverage
4 1224.4 (CACHE_DIR="$HOME/misc_cache" MINICONDA_DIR="$HOME/miniconda" PIP_DIR="$HOME/virtualenv" GATK_PATH="$CACHE_DIR" PYTHONIOENCODING=UTF8 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 kmer_utils --cov reports --cov taxon_filter --cov tools --cov util --cov file_utils" DOCKER_REGISTRY="quay.io" DOCKER_REPO_PROD="quay.io/broadinstitute/viral-ngs" DOCKER_REPO_DEV="quay.io/broadinstitute/viral-ngs-dev" DOCKER_REGISTRY_MIRROR="docker.io" DOCKER_REPO_PROD_MIRROR="broadinstitute/viral-ngs" BOTO_CONFIG=/dev/null _JAVA_OPTIONS="-Xmx3g" TRAVIS_JOB=test_py36) 28 Mar 2020 12:11AM UTC 0
72.96
Travis Job 1224.4
5 1224.5 (CACHE_DIR="$HOME/misc_cache" MINICONDA_DIR="$HOME/miniconda" PIP_DIR="$HOME/virtualenv" GATK_PATH="$CACHE_DIR" PYTHONIOENCODING=UTF8 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 kmer_utils --cov reports --cov taxon_filter --cov tools --cov util --cov file_utils" DOCKER_REGISTRY="quay.io" DOCKER_REPO_PROD="quay.io/broadinstitute/viral-ngs" DOCKER_REPO_DEV="quay.io/broadinstitute/viral-ngs-dev" DOCKER_REGISTRY_MIRROR="docker.io" DOCKER_REPO_PROD_MIRROR="broadinstitute/viral-ngs" BOTO_CONFIG=/dev/null _JAVA_OPTIONS="-Xmx3g" TRAVIS_JOB=test_snakemake) 28 Mar 2020 12:06AM UTC 0
23.26
Travis Job 1224.5
Source Files on build 1224
Detailed source file information is not available for this build.
  • Back to Repo
  • Build #1224
  • 266617b7 on github
  • Next Build on ct-single-end-bwa-deplete (#1226)
STATUS · Troubleshooting · Open an Issue · Sales · Support · CAREERS · ENTERPRISE · START FREE · SCHEDULE DEMO
ANNOUNCEMENTS · TWITTER · TOS & SLA · Supported CI Services · What's a CI service? · Automated Testing

© 2025 Coveralls, Inc