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Ascat #722

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Feb 1, 2019
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Ascat #722

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2 changes: 2 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- [#694](https://github.com/SciLifeLab/Sarek/pull/694) - Add monochrome and grey logos for light or dark background
- [#698](https://github.com/SciLifeLab/Sarek/pull/698) - Add btb profile for munin server
- [#702](https://github.com/SciLifeLab/Sarek/pull/702) - Add font-ttf-dejavu-sans-mono `2.37` and fontconfig `2.12.6` to container
- [#722](https://github.com/SciLifeLab/Sarek/pull/722) - Update `Sarek-data` submodule
- [#722](https://github.com/SciLifeLab/Sarek/pull/722) - Add path to ASCAT `.gc` file in `igenomes.config`

### `Changed`

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1 change: 1 addition & 0 deletions conf/genomes.config
Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@ params {
}
'smallGRCh37' {
acLoci = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci"
acLociGC = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci.gc"
dbsnp = "${params.genome_base}/dbsnp_138.b37.small.vcf"
dbsnpIndex = "${dbsnp}.idx"
genomeFile = "${params.genome_base}/human_g1k_v37_decoy.small.fasta"
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3 changes: 3 additions & 0 deletions conf/igenomes.config
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ params {
genomes {
'GRCh37' {
acLoci = "${params.genome_base}/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci"
acLociGC = "${params.genome_base}/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci.gc"
dbsnp = "${params.genome_base}/Annotation/GATKBundle/dbsnp_138.b37.vcf"
dbsnpIndex = "${params.genome_base}/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx"
genomeFile = "${params.genome_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta"
Expand All @@ -30,6 +31,7 @@ params {
}
'GRCh38' {
acLoci = "${params.genome_base}/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci"
acLociGC = "${params.genome_base}/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci.gc"
dbsnp = "${params.genome_base}/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz"
dbsnpIndex = "${params.genome_base}/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
genomeFile = "${params.genome_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta"
Expand All @@ -43,6 +45,7 @@ params {
}
'smallGRCh37' {
acLoci = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci"
acLociGC = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci.gc"
dbsnp = "${params.genome_base}/dbsnp_138.b37.small.vcf"
dbsnpIndex = "${dbsnp}.idx"
genomeFile = "${params.genome_base}/human_g1k_v37_decoy.small.fasta"
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