Update blacklist files

[JoseEspinosa]

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

[drpatelh]

Silly question but did you make sure the chromosomes match between the assembly genome fasta and the bed files? The files are generally provided relative to the UCSC whereas we use ENSEMBL in most places.

[JoseEspinosa]

No I didn't 😭
The only thing to do is to replace the chromosome identifiers or there is something else?

[drpatelh]

Documented commands for how we download the blacklists:

cd ..
mkdir -p v1.0
cd v1.0
wget -L https://www.encodeproject.org/files/ENCFF001TDO/@@download/ENCFF001TDO.bed.gz && gunzip ENCFF001TDO.bed.gz && mv ENCFF001TDO.bed hg19-blacklist.v1.bed

mkdir -p assets/blacklists/v2.0/
cd assets/blacklists/v2.0/
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/ce10-blacklist.v2.bed.gz && gunzip ce10-blacklist.v2.bed.gz
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/ce11-blacklist.v2.bed.gz && gunzip ce11-blacklist.v2.bed.gz
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/dm3-blacklist.v2.bed.gz && gunzip dm3-blacklist.v2.bed.gz
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/dm6-blacklist.v2.bed.gz && gunzip dm6-blacklist.v2.bed.gz
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/hg19-blacklist.v2.bed.gz && gunzip hg19-blacklist.v2.bed.gz
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/hg38-blacklist.v2.bed.gz && gunzip hg38-blacklist.v2.bed.gz
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/mm10-blacklist.v2.bed.gz && gunzip mm10-blacklist.v2.bed.gz

cd ..
mkdir -p v3.0
cd v3.0
wget -L https://www.encodeproject.org/files/ENCFF356LFX/@@download/ENCFF356LFX.bed.gz && gunzip ENCFF356LFX.bed.gz && mv ENCFF356LFX.bed hg38-blacklist.v3.bed

TODO

• v1.0 - hg19-blacklist.v1.bed -> GRCh37-blacklist.v1.bed (rename original version for GRCh37)
• v2.0 - mm10-blacklist.v2.bed -> GRCm38-blacklist.v2.bed
• v3.0 - hg38-blacklist.v3.bed -> GRCh38-blacklist.v3.bed

[JoseEspinosa]

Closed in favor of #255 and #257