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Add R64-1-1 and UMD3.1 #856

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merged 9 commits into from
Nov 21, 2022
Merged

Add R64-1-1 and UMD3.1 #856

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f432c2d
Merge remote-tracking branch 'upstream/dev' into dev
maxulysse Nov 15, 2022
80f6da8
add R64-1-1 for annotation
maxulysse Nov 21, 2022
16954f7
Merge branch 'nf-core:dev' into dev
maxulysse Nov 21, 2022
fbe1cbd
Merge branch 'nf-core:master' into dev_add_R64-1-1
maxulysse Nov 21, 2022
83aa1c5
Merge branch 'nf-core:dev' into dev
maxulysse Nov 21, 2022
ae998bf
Merge branch 'dev' into dev_add_R64-1-1
maxulysse Nov 21, 2022
73f07d5
update CHANGELOG
maxulysse Nov 21, 2022
7c6be8c
add bos_taurus_UMD3.1
maxulysse Nov 21, 2022
e11b18e
update CHANGELOG
maxulysse Nov 21, 2022
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Added

- [#856](https://github.com/nf-core/sarek/pull/856) - Add annotation for `R64-1-1` and `UMD3.1`

### Changed

- [#855](https://github.com/nf-core/sarek/pull/855) - Speed up duplicate marking by using `samtools` for CRAM conversion
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14 changes: 14 additions & 0 deletions conf/igenomes.config
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Expand Up @@ -138,6 +138,13 @@ params {
bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
snpeff_db = 'UMD3.1.75'
snpeff_genome = 'UMD3.1'
snpeff_version = '5.1'
vep_cache_version = 94
vep_genome = 'UMD3.1'
vep_species = 'bos_taurus'
vep_version = '106.1'
}
'WBcel235' {
bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
Expand Down Expand Up @@ -214,6 +221,13 @@ params {
'R64-1-1' {
bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
snpeff_db = 'R64-1-1.105'
snpeff_genome = 'R64-1-1'
snpeff_version = '5.1'
vep_cache_version = 106
vep_genome = 'R64-1-1'
vep_species = 'saccharomyces_cerevisiae'
vep_version = '106.1'
}
'EF2' {
bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
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