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Update to Innuca's recipe modules #191

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Update to Innuca's recipe modules #191

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Commits on Jan 8, 2019

  1. integrity_coverage template now checks the integrity of the read file… 

    …s with the appropriate compressing software. Added new directive with container
    @cimendes
    cimendes committed Jan 8, 2019
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Commits on Jan 9, 2019

  1. update container to integrity_coverage

    @cimendes
    cimendes committed Jan 9, 2019
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  2. added template mlst. Increases discriminatory power to the verificati… 

    …on of the expected species vs schema species

Co-authored-by: cimendes <iines.mendes@gmail.com>
Co-authored-by: miguelpmachado <mpmachado@fc.ul.pt>
    @cimendes @miguelpmachado
    cimendes and miguelpmachado committed Jan 9, 2019
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  3. fix typo

    @cimendes
    cimendes committed Jan 9, 2019
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Commits on Jan 10, 2019

  1. add insert_size template 

    - add sampel id to novel alleles file
    @cimendes
    cimendes committed Jan 10, 2019
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Commits on Jan 11, 2019

  1. added new retry to re-filter only by gc if assembly size is lower tha… 

    …n the 80% threshold.
    @cimendes
    cimendes committed Jan 11, 2019
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  2. verifies the % of mapped reads, issuing an warning when it falls 

    bellow 95%
    @cimendes
    cimendes committed Jan 11, 2019
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Commits on Jan 14, 2019

  1. new container directive for mlst process. 

    If expected species parameter not provided, bypasses the species verification control.
    @cimendes
    cimendes committed Jan 14, 2019
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Commits on Jan 15, 2019

  1. fix typo

    @cimendes
    cimendes committed Jan 15, 2019
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Commits on Jan 16, 2019

  1. update true_coverage image

    @cimendes
    cimendes committed Jan 16, 2019
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Commits on Jan 22, 2019

  1. Merge branch 'dev' into innuca_update

    @cimendes
    cimendes committed Jan 22, 2019
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  2. add insert_size to innuca's recipe. 

    set columBar to False in mlst .report.json
    @cimendes
    cimendes committed Jan 22, 2019
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Commits on Jan 23, 2019

  1. Fix typo in changelog.md 

    Co-Authored-By: cimendes <cimendes@users.noreply.github.com>
    @tiagofilipe12 @cimendes
    tiagofilipe12 and cimendes committed Jan 23, 2019
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  2. update changelog

    @cimendes
    cimendes committed Jan 23, 2019
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  3. Update changelog.md

    @cimendes
    cimendes committed Jan 23, 2019
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  4. Update flowcraft/generator/components/mapping.py 

    Co-Authored-By: cimendes <cimendes@users.noreply.github.com>
    @tiagofilipe12 @cimendes
    tiagofilipe12 and cimendes committed Jan 23, 2019
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  5. update inser_size output type

    @cimendes
    cimendes committed Jan 23, 2019
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  6. Update flowcraft/templates/insert_size.py 

    Co-Authored-By: cimendes <cimendes@users.noreply.github.com>
    @tiagofilipe12 @cimendes
    tiagofilipe12 and cimendes committed Jan 23, 2019
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Commits on Jan 26, 2019

  1. code cleanup

    @cimendes
    cimendes committed Jan 26, 2019
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Commits on Feb 6, 2019

  1. Update to fastQC rules for emitting warning and fail messages.

    @cimendes
    cimendes committed Feb 6, 2019
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