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Update pipeline blacklists #249

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Update blacklists when new versions are available as discussed on #228
The previous versions of blacklists have been moved to ./assets/blacklists/v1.0 folder.
The files in assets/blacklists/v2.0 were obtained from the The ENCODE Blacklist Github repo.
The file in ./assets/blacklists/v3.0 was downloaded from: https://sites.google.com/site/anshulkundaje/projects/blacklists
The new structure of the blacklist folder is:

.
├── v1.0
│   ├── GRCh37-blacklist.bed
│   ├── GRCm38-blacklist.bed
│   ├── hg19-blacklist.bed
│   ├── hg38-blacklist.bed
│   └── mm10-blacklist.bed
├── v2.0
│   ├── ce10-blacklist.v2.bed
│   ├── dm6-blacklist.v2.bed
│   ├── hg19-blacklist.v2.bed
│   ├── hg38-blacklist.v2.bed
│   └── mm10-blacklist.v2.bed
└── v3.0
    └── GRCh38_unified_blacklist.v3.bed

Closes #228

PR checklist

  • This comment contains a description of changes (with reason)
  • If you've fixed a bug or added code that should be tested, add tests!
  • If necessary, also make a PR on the nf-core/chipseq branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Make sure your code lints (nf-core lint .).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

@JoseEspinosa JoseEspinosa marked this pull request as ready for review February 2, 2022 17:24
@JoseEspinosa JoseEspinosa requested review from drpatelh and removed request for drpatelh February 2, 2022 22:30
@JoseEspinosa JoseEspinosa deleted the update_blacklist branch September 16, 2024 12:52
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