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coverage: 32.236% (-0.02%) from 32.251%
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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Add WDL for iSNVs/v-phaser (#828)

* sample names now optional for merge_to_vcf; bugfix for multi-chr v-phaser output

merge_to_vcf did not previously output correct alternate genotype number for some cases of multi-chr v-phaser output (line intrahost.py:820 of this commit). This corrects that and changes test cases to use the chr "-#" encoding to denote chromosome/segment number. This also changes merge_to_vcf so sample names are guessed from first column of v-phaser output if sample names are not passed in via --samples.

* add isnvs_per_sample to the end of two new WDL assembly workflows

* WDL isnv/vphaser WIP

add dummy workflows to support newer cromwell that requires WDL files to have a workflow block; add single-sample isnv workflows

* pass inputs to align_and_plot WDL

* add commas to WDL

* hide womtool PATH check stderr

* additional debug text for WDL building to DNAnexus

* debug

* rename isnv workflow WDL

* remove debug

* update dx-toolkit

* debug: comment out exit-on-error in build-dx

* force compile dxWDL

* upgrade cromwell, dxWDL

* move dummy workflow in reports.wdl

* remove dummy workflows from task files

* add some missing workflow inputs to assemble_denovo.wdl

* restore dummy workflows to WDL task files

restore dummy workflows to WDL task files; this allows womtool to validate them

* add compulsory inputs to WDL workflows to satisfy newer versions of cromwell and dxWDL

* more required inputs for WDL workflows; unique dummy workflow names

Note: this is WDL draft-2. Changing to WDL 1.0 will require various changes, starting with a "version 1.0" statement as the first line in each WDL. Also, input {} blocks. See: https://github.com/openwdl/wdl/blob/master/versions/1.0/SPEC.md

* use dummyworkflows as needed, remove from task WDLs

* remap dx default files; rename isnvs_per_sample -> isnvs_one_sample

* remap dx defaults for optional files

* add dx default file input... (continued)

2007 of 6226 relevant lines covered (32.24%)

0.32 hits per line

Source Files on job 6141.6 (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])