broadinstitute / viral-ngs / 6216 / 6
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coverage: 32.726%. Remained the same
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]

push

travis-ci

web-flow 
<a href="https://github.com/broadinstitute/viral-ngs/commit/<a class=hub.com/broadinstitute/viral-ngs/commit/a30825cdbf2940969181c8815d4a9ed48b9c5743">a30825cdb<a href="https://github.com/broadinstitute/viral-ngs/commit/a30825cdbf2940969181c8815d4a9ed48b9c5743">&quot;&gt;mlin&amp;#39;s new demux launcher (#838)

* import wip

* wip

* wip

* wip

* wip

* wip

* wip

* wip

* wip

* wip

* wip

* wip

* wip

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* Update demux_launcher.yml

* wip

* wip

* Revert &amp;quot;wip&quot;

This reverts commit </a><a class="double-link" href="https://github.com/broadinstitute/viral-ngs/commit/<a class="double-link" href="https://github.com/broadinstitute/viral-ngs/commit/037cf6b52277bbd3f8384e9096259d51682f1701">037cf6b52</a>">037cf6b52</a><a href="https://github.com/broadinstitute/viral-ngs/commit/a30825cdbf2940969181c8815d4a9ed48b9c5743">.

* wip

* Create README.md

* Update README.md

* Update README.md

* wip

* Update README.md

* add demux autoscaling to mlin&#39;s launcher

* place L# lane dirs under reads/; give applet title

* comment out auto-scaling for now

comment out auto-scaling, since each task in the resulting workflow seem s to inheir the instance type specified rather than use the on specified in the task runtime block

* set dx-jobutil-add-output class to jobref for subjob propagation call

* rename inputs to reflect WDLs with workflow-level inputs

* rename demux input

* reintroduce (stage-specific) autoscaling, set Q20 min base Q for NovaSeq runs, change demux_outputs class to array:file

* mem1_hdd2_x32 -&gt; mem1_ssd2_x36

* change instance type escaping

* change workflow instance type mapping spec (key=val for workflows)

* debug file propagation

* remove array spec from output aggregation

* jobref array

* reduce demux threads for NovaSeq case; propagate based on jobref

* change output field name in applet spec

* remove TODO comment

* change output collection class types

* revert to array:file

* restore array:file in propagate_outputs

* only propagate files, and only from the reads subdir

* dxWDL 0.68.1 -> 0.69

* decrease instance size a bit for HiSeq4k demux

2047 of 6255 relevant lines covered (32.73%)

0.33 hits per line

Source Files on job 6216.6 (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])