Code

Control-FREEC improvements#204

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Merged

maxulysse merged 34 commits intonf-core:devnf-core/sarek:devfrom maxulysse:ControlFREECmaxulysse/nf-core_sarek:ControlFREECCopy head branch name to clipboardMay 18, 2020

+697-541

Commits

Commits on May 15, 2020

• added script to help downstream analysis, adding RankScore for Scout

  

  Szilveszter Juhos

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  maxulysse

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  cb13187

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• nf-core bump-version . 2.5.1

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  maxulysse

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• reducing CPU usage for Mpileup

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  Szilveszter Juhos

  and

  maxulysse

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  fc1dd2f

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• First time CF is working with extra pileups

  

  Szilveszter Juhos

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  maxulysse

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  3b11389

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• yet an other version that somehow worked

  

  Szilveszter Juhos

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  maxulysse

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• remove --normal_pileup and --tumor_pileup params

  maxulysse

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• update freebayes germline command

  

  ggabernet

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  fad7a6a

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• update changelog

  

  ggabernet

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  maxulysse

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  3929a67

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• fix --save_bam_mapped + small typos

  maxulysse

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  5a62d50

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• update CHANGELOG

  maxulysse

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  455fd06

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• add step controlfreec

  maxulysse

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  815c36e

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• use nf-core header

  maxulysse

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  fa09b3d

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• update config

  maxulysse

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  b46f4e2

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• cleanup

  maxulysse

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  5f6eabc

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• add mappability files to igenomes

  maxulysse

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• better name for tsv file

  maxulysse

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  e5a27b4

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• fix output directory

  maxulysse

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  c514c3f

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• enable usage of - in names of tools or steps

  maxulysse

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  50a584c

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• better default for coefficientofvariation

  maxulysse

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  38dd289

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• improve help

  maxulysse

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  c7aec1a

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• First working version

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  Szilveszter Juhos

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  maxulysse

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  5d9e995

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• Fixing some null parameters and C&P typos

  

  Szilveszter Juhos

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  maxulysse

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  1983576

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• update and reorder params

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  1ca1c5a

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• reorder and update params

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  57cfad7

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• update and reorder params

  maxulysse

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  1692e5a

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• update docs

  maxulysse

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  cda438b

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• fix prepare_recalibration step

  maxulysse

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  4a1cf40

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• update CHANGELOG

  maxulysse

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  5b5d1dc

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• Apply suggestions from code review

  maxulysse

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  4e0a5f5

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• use only one cpu to generate mpileup for controlfreec

  maxulysse

  committed
  f59bcd0

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• fix conflicts

  maxulysse

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  23c2086

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• spacing

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• fix merge conflicts

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Commits on May 18, 2020

• if step = controlfreec then tools is controlfreec

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