Wran 1618 update annot beds - Githubissues

ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline

MIT License

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Wran 1618 update annot beds #164

Closed leepc12 closed 4 years ago

leepc12 commented 4 years ago

Output slightly changed due to change of blacklist. No output change in alignment.

Updated reference genome data (genome TSV file v3)

Link to ENCODE portal's URLs (instead of GCS mirror) of accessioned genome data.
New blacklist for GRCh38.
New TSS files (generated from GENCODE annotation GTF file) for GRCh38 and mm10
Repacked (with gzip -n) 6-col annotation BED files
- Promoter
- Enhancer
- DNase (Universal DHS regions)

Updated bash scripts to download/build reference genome dataset.

Updated circleci workflow-testing to use Caper instead of raw Cromwell.

Refactored config YAML
Worked around Bash conditional one-liner problem