Code

RNA workflow#500

Code

Draft

dennishendriksen wants to merge 16 commits intomainmolgenis/vip:mainfrom feat/rna_workflowmolgenis/vip:feat/rna_workflowCopy head branch name to clipboard

+25,060-4

Commits

Commits on Aug 3, 2023

• created a subworkflow for rna bam files, added data input and conversion

  RienkHeins

  committed
  4bca8bc

  Copy full SHA for 4bca8bc

Commits on Aug 9, 2023

• added rna subworkflow

  RienkHeins

  committed
  b09953c

  Copy full SHA for b09953c

• added rna bam files option into sample sheet

  RienkHeins

  committed
  7929ac5

  Copy full SHA for 7929ac5

Commits on Sep 5, 2023

• fixed rna variable and added featureCounts and outrider processes

  RienkHeins

  committed
  05fd44d

  Copy full SHA for 05fd44d

Commits on Sep 8, 2023

• updated featureCounts processes, now converting to count matrix for each sample

  RienkHeins

  committed
  fc66324

  Copy full SHA for fc66324

Commits on Sep 13, 2023

• completed featureCounts workflow and scripts

  RienkHeins

  committed
  1bda9ff

  Copy full SHA for 1bda9ff

Commits on Sep 19, 2023

• outrider implemented, fixed count matrix merge out of memory issue for larger datasets

  RienkHeins

  committed
  e7cf557

  Copy full SHA for e7cf557

Commits on Sep 25, 2023

• updated featurecounts, removed output error outrider, updated rna result process

  RienkHeins

  committed
  0b73b89

  Copy full SHA for 0b73b89

Commits on Sep 28, 2023

• Added gene name conversion from ensemble gene to gene ID, updated process resource management, added groovy functions

  RienkHeins

  committed
  01d4c0f

  Copy full SHA for 01d4c0f

Commits on Sep 29, 2023

• added text file containing code created for project

  RienkHeins

  committed
  f2e9de5

  Copy full SHA for f2e9de5

Commits on Oct 17, 2023

• Updated fastq workflow, added rule changes, updated config

  RienkHeins

  committed
  50262dc

  Copy full SHA for 50262dc

• updated vcf workflow, created parameters for processes, updated config

  RienkHeins

  committed
  f36a88f

  Copy full SHA for f36a88f

• added scripts used for optimization of the autoencoder

  RienkHeins

  committed
  77c35f3

  Copy full SHA for 77c35f3

• added script used for analysis of outrider results

  RienkHeins

  committed
  0b6bb0b

  Copy full SHA for 0b6bb0b

• added containers and explenatory files

  RienkHeins

  committed
  f2d8ed4

  Copy full SHA for f2d8ed4

• added notebook results and drop env file

  RienkHeins

  committed
  c7010a9

  Copy full SHA for c7010a9