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fix: genome typoes
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@dnousome
dnousome committed Jun 12, 2024
1 parent 5f54097 commit 0007ec3
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Showing 2 changed files with 12 additions and 12 deletions.
2 changes: 1 addition & 1 deletion conf/containers.config
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,6 @@ params {
vcf2maf = 'docker://dnousome/ccbr_vcf2maf:v102.0.0'
lofreq = 'docker://dnousome/ccbr_lofreq:v0.0.1'
octopus = 'docker://dancooke/octopus:latest'
annotcnvsv = 'docker://dnousome/ccbr_annotate_cnvsv:latest:v0.0.1'
annotcnvsv = 'docker://dnousome/ccbr_annotate_cnvsv:v0.0.1'
}
}
22 changes: 11 additions & 11 deletions conf/genomes.config
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,9 @@ params {
KNOWNINDELS = "-known /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -known /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz"
KNOWNRECAL = '--known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GATK_resource_bundle/dbsnp_138.hg38.vcf.gz --known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GATK_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GATK_resource_bundle/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz'
dbsnp = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/dbsnp_138.hg38.vcf.gz"
gnomad = '--germline-resource /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz' // /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz
gnomad = '--germline-resource /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz'
pon = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/PON/updatedpon.vcf.gz" //pon="/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/PON/hg38.noCOSMIC_ClinVar.pon.vcf.gz" //file{params.pon}
kgp = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz"
germline_resource = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz"
KRAKENBACDB = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/kraken/20180907_standard_kraken2"
snpeff_genome = "GRCh38.86"
snpeff_config = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/snpEff/4.3t/snpEff.config"
Expand Down Expand Up @@ -46,15 +46,15 @@ params {
genome = "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19.with_extra.fa"
genomefai = "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19.with_extra.fa.fai"
bwagenome= "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.fa"
genomedict= "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.dict"
genomedict= "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19.with_extra.dict"
intervals= "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg19/hg19_noblacklist_maincontig.bed"
INDELREF = "/fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf" //ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz"
KNOWNINDELS = "-known /fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -known /fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf"
KNOWNRECAL = '--known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GATK_resource_bundle/dbsnp_138.hg38.vcf.gz --known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GATK_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GATK_resource_bundle/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz'
INDELREF = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg19/GATKbundle/Mills_and_1000G_gold_standard.indels.hg19.vcf.gz"
KNOWNINDELS = "-known /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg19/GATKbundle/Mills_and_1000G_gold_standard.indels.hg19.vcf.gz -known /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg19/GATKbundle/1000G_phase1.indels.hg19.vcf.gz"
KNOWNRECAL = '--known-sites /fdb/GATK_resource_bundle/hg19-2.8/dbsnp_138.hg19.excluding_sites_after_129.vcf.gz --known-sites /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg19/GATKbundle/Mills_and_1000G_gold_standard.indels.hg19.vcf.gz'
dbsnp = "/fdb/GATK_resource_bundle/hg19-2.8/dbsnp_138.hg19.vcf.gz"
gnomad = '--germline-resource /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz' // /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz
pon = "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh37.noCOSMIC_ClinVar.pon.vcf.gz"
kgp = "/fdb/GATK_resource_bundle/hg19-2.8/dbsnp_138.hg19.vcf.gz"
germline_resource = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg19/GATKbundle/af-only-gnomad.raw.sites.liftover.hg19.vcf.gz"
gnomad = '--germline-resource /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg19/GATKbundle/af-only-gnomad.raw.sites.liftover.hg19.vcf.gz'
pon = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg19/GATKbundle/hg19.liftGRCh37.noCOSMIC_ClinVar.pon.vcf.gz"
KRAKENBACDB = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/kraken/20180907_standard_kraken2"
snpeff_genome = "GRCh37.75"
snpeff_config = "/usr/local/apps/snpEff/4.3t/snpEff.config"
Expand Down Expand Up @@ -94,9 +94,9 @@ params {
KNOWNRECAL = "-known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/dbsnp/mm10_known_indels.vcf.gz -known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/dbsnp/mm10_known_snps.vcf.gz"
dbsnp = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/dbsnp/mm10_allstrains_dbSNP142.vcf.gz"
pon = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/dbsnp/mm10_dbSNP_allStrains_compSet_noIND.vcf.gz"
kgp = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/dbsnp/mm10_knownSNPs_sites.vcf.gz"
KRAKENBACDB = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/kraken/20180907_standard_kraken2"
germline_resource = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/dbsnp/mm10_knownSNPs_sites.vcf.gz"
gnomad= "--germline-resource /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/dbsnp/mm10_allstrains_dbSNP142.vcf.gz"
KRAKENBACDB = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/kraken/20180907_standard_kraken2"
snpeff_genome = "GRCm38.86"
snpeff_config = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/snpEff/4.3t/snpEff.config"
snpeff_bundle = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/snpEff/4.3t/"
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