Code

ChromHMM enhancer extension#68

Code

Merged

nictru merged 22 commits intoinspectdaisybio/TF-Prioritizer:inspectfrom inspect-chromhmmdaisybio/TF-Prioritizer:inspect-chromhmmCopy head branch name to clipboardJan 24, 2024

+1,106-15

Commits

Commits on Dec 7, 2023

• Switch to RData based approach in ehmm

  nictru

  committed
  eb4d9ea

  Copy full SHA for eb4d9ea

• Added initial chromHMM workflow

  

  LeonHafner

  authored and

  nictru

  committed
  8820918

  Copy full SHA for 8820918

• Added ChromHMM GET_OUTPUT

  LeonHafner

  committed
  60a6bc9

  Copy full SHA for 60a6bc9

• Added openjdk docker container

  LeonHafner

  committed
  86cd8c9

  Copy full SHA for 86cd8c9

Commits on Dec 8, 2023

• Added process labels

  LeonHafner

  committed
  0584335

  Copy full SHA for 0584335

Commits on Dec 13, 2023

• Removed obsolete ChromHMM files and added chromsizes to igenomes config

  LeonHafner

  committed
  5a05bc0

  Copy full SHA for 5a05bc0

• Removed regular (non igenomes) chromsizes files

  LeonHafner

  committed
  95a1d91

  Copy full SHA for 95a1d91

• Moved ChromHMM executable to bin

  LeonHafner

  committed
  39e3df9

  Copy full SHA for 39e3df9

• Added metadata propagation to chromhmm

  LeonHafner

  committed
  2d8f9a5

  Copy full SHA for 2d8f9a5

Commits on Dec 26, 2023

• Modified ignore files

  LeonHafner

  committed
  6d15e8b

  Copy full SHA for 6d15e8b

• Integrated ChromHMM into pipeline

  LeonHafner

  committed
  bcd52b6

  Copy full SHA for bcd52b6

• Added ChromHMM docker container

  LeonHafner

  committed
  8c6c89e

  Copy full SHA for 8c6c89e

Commits on Jan 6, 2024

• Added ROSE workflow

  LeonHafner

  committed
  ef90358

  Copy full SHA for ef90358

• Added more ucsc files to igenomes

  LeonHafner

  committed
  900bb75

  Copy full SHA for 900bb75

Commits on Jan 9, 2024

• Added stub to RUN_ROSE

  LeonHafner

  committed
  7b7f492

  Copy full SHA for 7b7f492

• Integrate output of Rose into workflow and disable eHMM

  LeonHafner

  committed
  6aa60a6

  Copy full SHA for 6aa60a6

Commits on Jan 15, 2024

• Changed shebang according to: https://stackoverflow.com/a/19305076

  LeonHafner

  committed
  7ba5e99

  Copy full SHA for 7ba5e99

Commits on Jan 17, 2024

• Replaced ROSE_OUTPUT_TO_BED with nf-core gawk

  LeonHafner

  committed
  86cc1b9

  Copy full SHA for 86cc1b9

• Removed obsolete ROSE_OUTPUT_TO_BED file

  LeonHafner

  committed
  10e5894

  Copy full SHA for 10e5894

Commits on Jan 18, 2024

• Replaced BED_TO_GFF with nf-core gawk

  LeonHafner

  committed
  a13bb24

  Copy full SHA for a13bb24

• Changed ROSE_OUTPUT_TO_BED output file name

  LeonHafner

  committed
  b2da525

  Copy full SHA for b2da525

• Replaced REFORMAT_GFF with nf-core gawk

  LeonHafner

  committed
  d94cb47

  Copy full SHA for d94cb47