Code

Add ApplyBQSR, SamtoolStats, BamQC#259

Code

Merged

FriederikeHanssen merged 14 commits intonf-core:dsl2nf-core/sarek:dsl2from FriederikeHanssen:add_indexFriederikeHanssen/sarek:add_indexCopy head branch name to clipboardAug 3, 2020

+203-513

Commits

Commits on Jul 30, 2020

• Add ApplyBQSR module

  FriederikeHanssen

  committed
  70dcb1b

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• Add ApplyBQSR process in WF

  FriederikeHanssen

  committed
  4fcb25a

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Commits on Jul 31, 2020

• Make samtools index separate process and sort with merge_bam

  FriederikeHanssen

  committed
  7c5f5b5

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• Add qualimap and samtools stats, remove useless comments

  FriederikeHanssen

  committed
  47636a8

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• Add qc to workflow

  FriederikeHanssen

  committed
  a876ba5

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• Remove everything sentenion, we can look it up later in the released main.nf

  FriederikeHanssen

  committed
  9f08a51

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• Some more small changes and removal of used code

  FriederikeHanssen

  committed
  ed2fc42

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• Add multiqc back in

  FriederikeHanssen

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  00de14c

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• Remove obsolet when statement

  FriederikeHanssen

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  6d12fb3

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• Comment tag back in

  FriederikeHanssen

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  fec9391

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• Add qualimap_bamqc back in

  FriederikeHanssen

  committed
  18e242a

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• Add conditional samtools stats

  FriederikeHanssen

  committed
  0f6151b

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• Traced the error to target_bed, however also the bam files are reportedly corrupted...

  FriederikeHanssen

  committed
  f18ecda

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• Merge_Bam_recal bams are the problem, other bams are fine

  FriederikeHanssen

  committed
  40e2adb

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