broadinstitute / viral-ngs / 6513
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Jobs 2
Files 48
Run time 15min
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add workflows for isnvs_merge_to_vcf (#864)

* add workflows for isnvs_merge_to_vcf and isnvs_merge_to_vcf_filtered

* consolidate isnv workflows

* include multiple alignment as part of isnv merge_to_vcf

* isnvs_per_sample: also remove ".mapped" from bam file used to infer sample name

* make emaill address optional for isnvs_vcf WDL (and for snpEff)

* infer snpEff accessions from ref fasta if not provided

* wdl corrections

* WIP

* chain commands with  &&; accession parse correction

* set -ex -o pipefail

* comment change

* update snpEff 4.1l -> 4.3.1t

* add snpEff integration test

* comment out custom tmpdir test fixtures

* try older tmpdir fixtures

* replace tmpdir_function fixture with tempfile.gettempdir()

* revert; incorporate changes from 0191d68 (@notestaff)

* only check final snp_eff tabular output

* disable stdout capture by pytest for snpeff test

* ignore BOM in open_or_gzopen

https://en.wikipedia.org/wiki/Byte_order_mark

* typo correction

* debug

* io open

* kwarg reorder

* debug

* revert utf-8-sig

* remove debug

* correct git merge butchery

* skip test_snpeff for now

errors occur on Travis that so far have not been reproducible locally

* dev notes

* allow passage of stderr handle in run_and_print

allow passage of stderr handle in run_and_print, defaulting to stdout redirection as before if not specified

* stderr=subprocess.STDOUT default in run_and_print

* py27 doesn't have subprocess.DEVNULL (thanks, @notestaff)

* correcting late night mistakes

* assertAlmostEqual for floats in snpEff test

* maintain consistent order of inferred sample name w/r/t isnv files

* WIP

* add --emailAddress syntax to snpEff snakemake rule

* WIP

* WIP

* remove test skipIf

51 of 51 new or added lines in 5 files covered. (100.0%)

6875 of 9296 relevant lines covered (73.96%)

0.96 hits per line

Jobs
ID Job ID Ran Files Coverage
5 6513.5 (TRAVIS_JOB=test_py36 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 --cov file_utils") 0
73.9
 Travis Job 6513.5
6 6513.6 (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 --cov file_utils") 0
32.29
 Travis Job 6513.6
Source Files on build 6513
Detailed source file information is not available for this build.