Code

Feat/umi tn#563

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Merged

ashwini06 merged 26 commits intodevelopClinical-Genomics/BALSAMIC:developfrom feat/umi_TNClinical-Genomics/BALSAMIC:feat/umi_TNCopy head branch name to clipboardFeb 18, 2021

+135-323

Commits

Commits on Feb 17, 2021

• umiextract rules changed to sample names

  

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  487d0de

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• rules consenuscall wildcrads set to sample names

  

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  57cbebd

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• seperate two input files commandlines

  

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• TNscope rules for paired analysis

  

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  3f7f580

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• fix umi collect hsmetric for multiqc

  

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  5f8ec7c

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• fix wildcards in qc_umi

  

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  00f1eee

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• fix align header to sample name

  

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  d1390ed

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• fix rules in main and umi workflows

  

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  5ded6fe

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• fix conditional statement for umi rules

  

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Commits on Feb 18, 2021

• removed get_densityplot function from workflowscripts.py

  

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  2274dc8

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• removed matplotlib and searborn packages

  

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  f2f8300

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• using only consensusfilter file for variantcalling

  

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  ef69f34

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• remove vardict variantcalling rule

  

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  5636a5c

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• removed rules bcftools_query_calculatenoiseAF_umi, seaborn_densityplot_umi and wildcard {step}

  

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  c72b98a

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• remove wildcard step for umi_collect_hsmetric

  

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  c3fccad

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• change umi variantcaller name to TNscope_umi in VCFdict

  

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  e4b8a66

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• fix missing . in tnscope output

  

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  9d5ffde

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• remove wildcard {step} and simplification in UMI workflow

  

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  a2cfa62

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• fix VCFModel for TNscope_umi

  

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• delete densityplot related test data files

  

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  e1c2f34

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• remove get_density_plot function from pytests

  

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  5dc9c74

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• refactor of umi related code lines in balsamic workflow

  

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  e8135c8

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• remove get_densityplot from test_utils

  

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  f636df9

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• remove density plots related test lines

  

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  c0c86cd

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• fix import name for get_file_contents

  

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  3c382cc

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• fix back the matplotlib.pyplot

  

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