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Moving pipeline resources to OpenOmics shared group area
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@skchronicles
skchronicles committed Jun 30, 2022
1 parent 755764d commit 1c9e442
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8 changes: 4 additions & 4 deletions config/containers.json
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{
"images": {
"base": "/data/NCBR/dev/SIFs/ccbr_wes_base_v0.1.0.sif",
"deepvariant": "/data/NCBR/dev/SIFs/deepvariant_1.3.0-gpu.sif",
"glnexus": "/data/NCBR/dev/SIFs/glnexus_v1.4.1.sif",
"open_cravat": "/data/NCBR/dev/SIFs/ncbr_opencravat_latest.sif"
"base": "/data/OpenOmics/SIFs/ccbr_wes_base_v0.1.0.sif",
"deepvariant": "/data/OpenOmics/SIFs/deepvariant_1.3.0-gpu.sif",
"glnexus": "/data/OpenOmics/SIFs/glnexus_v1.4.1.sif",
"open_cravat": "/data/OpenOmics/SIFs/ncbr_opencravat_latest.sif"
}
}
34 changes: 17 additions & 17 deletions config/genome.json
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{
"references": {
"ANNOTSV_BUILD": "GRCh38",
"CANVAS_GENOME": "/data/NCBR/references/genome-seek/CANVAS/WholeGenomeFasta",
"CANVAS_KMER": "/data/NCBR/references/genome-seek/CANVAS/kmer.fa",
"CANVAS_FILTER": "/data/NCBR/references/genome-seek/CANVAS/filter13.bed",
"CANVAS_BALLELES": "/data/NCBR/references/genome-seek/CANVAS/dbsnp.vcf",
"CANVAS_GENOME": "/data/OpenOmics/references/genome-seek/CANVAS/WholeGenomeFasta",
"CANVAS_KMER": "/data/OpenOmics/references/genome-seek/CANVAS/kmer.fa",
"CANVAS_FILTER": "/data/OpenOmics/references/genome-seek/CANVAS/filter13.bed",
"CANVAS_BALLELES": "/data/OpenOmics/references/genome-seek/CANVAS/dbsnp.vcf",
"CHR_CHUNKS": [
"chr1", "chr2", "chr3", "chr4", "chr5",
"chr6", "chr7", "chr8", "chr9", "chr10",
"chr11", "chr12", "chr13", "chr14", "chr15",
"chr16", "chr17", "chr18", "chr19", "chr20",
"chr21", "chr22", "chrX", "chrY", "chrM"
],
"GENOME": "/data/NCBR/references/genome-seek/Homo_sapiens_assembly38.fasta",
"GENOME": "/data/OpenOmics/references/genome-seek/Homo_sapiens_assembly38.fasta",
"FASTQ_SCREEN_CONFIG": "resources/fastq_screen.conf",
"FASTQC_ADAPTERS": "resources/fastqc_adapters.tsv",
"DBSNP": "/data/NCBR/references/genome-seek/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
"DBSNP": "/data/OpenOmics/references/genome-seek/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
"KNOWNINDELS": [
"/data/NCBR/references/genome-seek/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"/data/NCBR/references/genome-seek/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz"
"/data/OpenOmics/references/genome-seek/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"/data/OpenOmics/references/genome-seek/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz"
],
"KNOWNRECAL": [
"/data/NCBR/references/genome-seek/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
"/data/NCBR/references/genome-seek/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"/data/NCBR/references/genome-seek/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz"
"/data/OpenOmics/references/genome-seek/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
"/data/OpenOmics/references/genome-seek/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"/data/OpenOmics/references/genome-seek/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz"
],
"NRECALS": {
"recal1": ["chr1", "chr2", "chr14", "chrY"],
Expand All @@ -32,16 +32,16 @@
"recal4": ["chr8", "chr9", "chr10", "chr13", "chr20"],
"recal5": ["chr11", "chr12", "chr17", "chr19", "chr22", "chrX"]
},
"MANTA_CALLREGIONS": "/data/NCBR/references/genome-seek/Manta/Homo_sapiens_assembly38_main_chromosomes.bed.gz",
"MANTA_CALLREGIONS": "/data/OpenOmics/references/genome-seek/Manta/Homo_sapiens_assembly38_main_chromosomes.bed.gz",
"OC_LIFTOVER": "hg38",
"OC_MODULES": "/data/NCBR/references/genome-seek/OpenCRAVAT/modules",
"OC_MODULES": "/data/OpenOmics/references/genome-seek/OpenCRAVAT/modules",
"PEDDY_FILTER": "chr22",
"SNPEFF_GENOME": "GRCh38.86",
"SNPEFF_CONFIG": "/data/NCBR/references/genome-seek/snpEff/4.3t/snpEff.config",
"SNPEFF_BUNDLE": "/data/NCBR/references/genome-seek/snpEff/4.3t/",
"SNPEFF_CONFIG": "/data/OpenOmics/references/genome-seek/snpEff/4.3t/snpEff.config",
"SNPEFF_BUNDLE": "/data/OpenOmics/references/genome-seek/snpEff/4.3t/",
"SOMALIER": {
"ANCESTRY_DB": "/data/NCBR/references/genome-seek/somalier/1kg-somalier",
"SITES_VCF": "/data/NCBR/references/genome-seek/somalier/sites.hg38.vcf.gz",
"ANCESTRY_DB": "/data/OpenOmics/references/genome-seek/somalier/1kg-somalier",
"SITES_VCF": "/data/OpenOmics/references/genome-seek/somalier/sites.hg38.vcf.gz",
"NCBI_BUILD": "GRCh38",
"SPECIES": "homo_sapiens"
}
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16 changes: 8 additions & 8 deletions resources/fastq_screen.conf
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#########
## Human - sequences available from
## ftp://ftp.ensembl.org/pub/current/fasta/homo_sapiens/dna/
DATABASE Human /data/NCBR/references/genome-seek/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38
DATABASE Human /data/OpenOmics/references/genome-seek/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38



#########
## Mouse - sequence available from
## ftp://ftp.ensembl.org/pub/current/fasta/mus_musculus/dna/
DATABASE Mouse /data/NCBR/references/genome-seek/FastQ_Screen_Genomes/Mouse/Mus_musculus.GRCm38
DATABASE Mouse /data/OpenOmics/references/genome-seek/FastQ_Screen_Genomes/Mouse/Mus_musculus.GRCm38


##########
## rRNA - In house custom database
DATABASE rRNA /data/NCBR/references/genome-seek/FastQ_Screen_Genomes/rRNA/GRCm38_rRNA
DATABASE rRNA /data/OpenOmics/references/genome-seek/FastQ_Screen_Genomes/rRNA/GRCm38_rRNA


##############
## Mitochondria
DATABASE MT /data/NCBR/references/genome-seek/FastQ_Screen_Genomes/Mitochondria/mitochondria
DATABASE MT /data/OpenOmics/references/genome-seek/FastQ_Screen_Genomes/Mitochondria/mitochondria


########
## PhiX - sequence available from Refseq accession NC_001422.1
DATABASE PhiX /data/NCBR/references/genome-seek/FastQ_Screen_Genomes/PhiX/phi_plus_SNPs
DATABASE PhiX /data/OpenOmics/references/genome-seek/FastQ_Screen_Genomes/PhiX/phi_plus_SNPs



##############
## Lambda
DATABASE Lambda /data/NCBR/references/genome-seek/FastQ_Screen_Genomes/Lambda/Lambda
DATABASE Lambda /data/OpenOmics/references/genome-seek/FastQ_Screen_Genomes/Lambda/Lambda



##########
## Vector - Sequence taken from the UniVec database
## http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
DATABASE Vectors /data/NCBR/references/genome-seek/FastQ_Screen_Genomes/Vectors/Vectors
DATABASE Vectors /data/OpenOmics/references/genome-seek/FastQ_Screen_Genomes/Vectors/Vectors



############
## Adapters - sequence derived from the FastQC contaminats file
## www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
DATABASE Adapters /data/NCBR/references/genome-seek/FastQ_Screen_Genomes/Adapters/Contaminants
DATABASE Adapters /data/OpenOmics/references/genome-seek/FastQ_Screen_Genomes/Adapters/Contaminants

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