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Releases: ENCODE-DCC/dnase-seq-pipeline

v3.0.0

11 Nov 02:46
@keenangraham keenangraham
v3.0.0
c1082e6
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v3.0.0 Latest
Latest

PIP-1449-add-alternate-runtimes (#90)
PIP-1429-return-peaks-starch (#88)
PIP-1410-update-images (#87)
PIP-1328-allow-gzipped-text-files-in-references (#85)
PIP-1304-use-ints-in-input (#84)

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v3.0.0-beta

20 Jul 23:57
@keenangraham keenangraham
v3.0.0-beta
ea8ce64
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v3.0.0-beta Pre-release
Pre-release

Same as v3.0.0-alpha.2 but results from following experiments validated by Stamlab:

  • ENCSR259GYP
  • ENCSR420RWU
  • ENCSR261RWJ
  • ENCSR277KRY
  • ENCSR426IEA
  • ENCSR931UQB
  • ENCSR508FVM
  • ENCSR693UHT
  • ENCSR323UTX
  • ENCSR000EPH
  • ENCSR149XIL
  • ENCSR894HWV
  • ENCSR216UMD
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v3.0.0-alpha.2

23 Jun 00:15
@keenangraham keenangraham
v3.0.0-alpha.2
8f8d57f
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v3.0.0-alpha.2 Pre-release
Pre-release
  • Use cutadapt for trimming adapters
  • Switch from Quay to Dockerhub
  • Set Java heap and GC threads in Picard MarkDuplicates
  • Pin Python 2 versions in Dockerfile
  • Update chrom_sizes filename in references.wdl
  • Output footprint dispersion model
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v3.0.0-alpha.1

19 May 02:26
@keenangraham keenangraham
v3.0.0-alpha.1
56fac50
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v3.0.0-alpha.1 Pre-release
Pre-release
  • Allow input of reference groups as tar.gz archives
  • Optionally apply blacklists to hotspot reference building step
  • Require explicit adapters sequences as input
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v3.0.0-alpha

08 May 02:12
@keenangraham keenangraham
v3.0.0-alpha
64c4baf
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v3.0.0-alpha Pre-release
Pre-release

This is the initial alpha release of the ENCODE DNase-seq pipeline. It is functionally similar to our old DNAnexus pipeline (https://github.com/ENCODE-DCC/dnase_pipeline/) but has been entirely rewritten in our reproducible WDL/Caper/Cromwell/Docker/testing framework. All tasks, subworkflows, and workflows have unit, integration, and functional tests, respectively. While many of the outputs and QC are similar we are additionally outputting 0.1% Hotspot2 peaks and 1% FDR footprints. It is based on the pipeline implemented by the Stam Lab in the stampipes repo (https://github.com/StamLab/stampipes).

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