broadinstitute / viral-ngs / 723

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travis-ci-com

add WDL task to aggregate spikein reports (#965)

* add WDL task to aggregate spikein reports

add WDL task to aggregate spikein reports; include this as part of demux_plus and demux_metag after scatter-gather creation of spikein reports

* remove unused input file

* debug info

* reorder a few WDL rules to account for input specified by stage for DNAnexus

* pin conda version

* typo

* conda install

* conda buildv3 compiler spec

* remove lengthy conda package list from build requirements

remove lengthy conda package list from conda recipe build requirements (it's still used for run requirements)

* debug statements

* escape jinja-spec compiler function

escape jinja-spec compiler function using jinja so conda can substitute the value after we render the recipe

* remove cruft

296 of 2629 branches covered (11.26%)

1453 of 6052 relevant lines covered (24.01%)

0.97 hits per line