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add workflows for isnvs_merge_to_vcf #864

Merged
merged 50 commits into from
Jul 25, 2018
Merged

add workflows for isnvs_merge_to_vcf #864

merged 50 commits into from
Jul 25, 2018

Commits on Jul 23, 2018

  1. add workflows for isnvs_merge_to_vcf and isnvs_merge_to_vcf_filtered

    @tomkinsc
    tomkinsc committed Jul 23, 2018
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  2. consolidate isnv workflows

    @tomkinsc
    tomkinsc committed Jul 23, 2018
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  3. Merge branch 'master' into ct-add-merge-to-vcf

    @tomkinsc
    tomkinsc authored Jul 23, 2018
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  4. include multiple alignment as part of isnv merge_to_vcf

    @tomkinsc
    tomkinsc committed Jul 23, 2018
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  5. Merge branch 'ct-add-merge-to-vcf' of ssh://github.com/broadinstitute… 

    …/viral-ngs into ct-add-merge-to-vcf
    @tomkinsc
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Commits on Jul 24, 2018

  1. Merge branch 'master' into ct-add-merge-to-vcf

    @tomkinsc
    tomkinsc authored Jul 24, 2018
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  2. isnvs_per_sample: also remove ".mapped" from bam file used to infer s… 

    …ample name
    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  3. Merge branch 'ct-add-merge-to-vcf' of ssh://github.com/broadinstitute… 

    …/viral-ngs into ct-add-merge-to-vcf
    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  4. make emaill address optional for isnvs_vcf WDL (and for snpEff)

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  5. infer snpEff accessions from ref fasta if not provided

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  6. Merge branch 'master' into ct-add-merge-to-vcf

    @tomkinsc
    tomkinsc authored Jul 24, 2018
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  7. wdl corrections

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  8. Merge branch 'ct-add-merge-to-vcf' of ssh://github.com/broadinstitute… 

    …/viral-ngs into ct-add-merge-to-vcf
    @tomkinsc
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  9. WIP

    @tomkinsc
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  10. chain commands with &&; accession parse correction

    @tomkinsc
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  11. set -ex -o pipefail

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  12. comment change

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  13. update snpEff 4.1l -> 4.3.1t

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  14. add snpEff integration test

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  15. comment out custom tmpdir test fixtures

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  16. try older tmpdir fixtures

    @tomkinsc
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  17. replace tmpdir_function fixture with tempfile.gettempdir()

    @tomkinsc
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  18. revert; incorporate changes from 0191d68 (@notestaff)

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  19. only check final snp_eff tabular output

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  20. disable stdout capture by pytest for snpeff test

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  21. ignore BOM in open_or_gzopen 

    https://en.wikipedia.org/wiki/Byte_order_mark
    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  22. typo correction

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  23. Merge branch 'master' into ct-add-merge-to-vcf

    @tomkinsc
    tomkinsc authored Jul 24, 2018
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  24. debug

    @tomkinsc
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  25. Merge branch 'ct-add-merge-to-vcf' of ssh://github.com/broadinstitute… 

    …/viral-ngs into ct-add-merge-to-vcf
    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  26. io open

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  27. kwarg reorder

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  28. debug

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  29. revert utf-8-sig

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  30. remove debug

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  31. Merge remote-tracking branch 'origin/master' into ct-add-merge-to-vcf

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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  32. correct git merge butchery

    @tomkinsc
    tomkinsc committed Jul 24, 2018
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Commits on Jul 25, 2018

  1. skip test_snpeff for now 

    errors occur on Travis that so far have not been reproducible locally
    @tomkinsc
    tomkinsc committed Jul 25, 2018
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  2. dev notes

    @tomkinsc
    tomkinsc committed Jul 25, 2018
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  3. 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
    @tomkinsc
    tomkinsc committed Jul 25, 2018
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  4. stderr=subprocess.STDOUT default in run_and_print

    @tomkinsc
    tomkinsc committed Jul 25, 2018
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  5. py27 doesn't have subprocess.DEVNULL (thanks, @notestaff)

    @tomkinsc
    tomkinsc committed Jul 25, 2018
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  6. correcting late night mistakes

    @tomkinsc
    tomkinsc committed Jul 25, 2018
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  7. assertAlmostEqual for floats in snpEff test

    @tomkinsc
    tomkinsc committed Jul 25, 2018
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  8. maintain consistent order of inferred sample name w/r/t isnv files

    @tomkinsc
    tomkinsc committed Jul 25, 2018
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  9. WIP

    @tomkinsc
    tomkinsc committed Jul 25, 2018
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  10. add --emailAddress syntax to snpEff snakemake rule

    @tomkinsc
    tomkinsc committed Jul 25, 2018
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  11. WIP

    @tomkinsc
    tomkinsc committed Jul 25, 2018
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  12. WIP

    @tomkinsc
    tomkinsc committed Jul 25, 2018
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  13. remove test skipIf

    @tomkinsc
    tomkinsc committed Jul 25, 2018
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