Skip to content

Commit

Permalink
Updated paths in input templates. Added examples for ref_map and tert…
Browse files Browse the repository at this point in the history 
…iary_map files.
  • Loading branch information
@williamrowell
williamrowell committed Aug 13, 2024
1 parent b801304 commit 0747310
Show file tree
Hide file tree
Showing 14 changed files with 108 additions and 12 deletions.
12 changes: 12 additions & 0 deletions backends/aws-healthomics/GRCh38.ref_map.v2p0p0-rc2.aws.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
name GRCh38
fasta s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.fasta
fasta_index s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai
pbsv_splits s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.pbsv_splits.json
pbsv_tandem_repeat_bed s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.trf.bed
trgt_tandem_repeat_bed s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed
hificnv_exclude_bed s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz
hificnv_exclude_bed_index s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz.tbi
hificnv_expected_bed_male s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/expected_cn.hg38.XY.bed
hificnv_expected_bed_female s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/expected_cn.hg38.XX.bed
pharmcat_positions_vcf s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/pharmcat/pharmcat_positions_2.15.0.vcf.bgz
pharmcat_positions_vcf_index s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/pharmcat/pharmcat_positions_2.15.0.vcf.bgz.csi
12 changes: 12 additions & 0 deletions backends/aws-healthomics/GRCh38.tertiary_map.v2p0p0-rc2.aws.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
slivar_js s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/slivar/slivar-functions.v0.2.8.js
ensembl_gff s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/ensembl.GRCh38.101.reformatted.gff3.gz
lof_lookup s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/slivar/lof_lookup.v2.1.1.txt
clinvar_lookup s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/slivar/clinvar_gene_desc.20240624T165443.txt
slivar_gnotate_files s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/slivar_gnotate/gnomad.hg38.v4.1.custom.v1.zip,s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/slivar_gnotate/CoLoRSdb.GRCh38.v1.1.0.deepvariant.glnexus.zip
slivar_gnotate_prefixes gnomad,colors
slivar_max_af 0.03
slivar_max_nhomalt 4
slivar_max_ac 4
slivar_min_gq 5
svpack_pop_vcfs s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz,s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.1.0.pbsv.jasmine.vcf.gz
svpack_pop_vcf_indices s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz.tbi,s3://pacbio-hifi-human-wgs-reference/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.1.0.pbsv.jasmine.vcf.gz.tbi
4 changes: 2 additions & 2 deletions backends/aws-healthomics/family.healthomics.inputs.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,9 @@
}
]
},
"humanwgs_family.ref_map_file": "s3://<bucket_path>/GRCh38.ref_map.v1.hpc.tsv",
"humanwgs_family.ref_map_file": "s3://<bucket_path>/GRCh38.ref_map.v2p0p0-rc2.azure.tsv",
"humanwgs_family.phenotypes": "String? (optional)",
"humanwgs_family.tertiary_map_file": "s3://<bucket_path>/GRCh38.tertiary_map.v2.hpc.tsv",
"humanwgs_family.tertiary_map_file": "s3://<bucket_path>/GRCh38.tertiary_map.v2p0p0-rc2.azure.tsv",
"humanwgs_family.backend": "AWS-HealthOmics",
"humanwgs_family.container_registry": "String",
"humanwgs_family.container_namespace": "String",
Expand Down
4 changes: 2 additions & 2 deletions backends/aws-healthomics/singleton.healthomics.inputs.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,9 @@
"humanwgs_singleton.hifi_reads": [
"File"
],
"humanwgs_singleton.ref_map_file": "s3://<bucket_path>/GRCh38.ref_map.v1.hpc.tsv",
"humanwgs_singleton.ref_map_file": "s3://<bucket_path>/GRCh38.ref_map.v2p0p0-rc2.azure.tsv",
"humanwgs_singleton.phenotypes": "String? (optional)",
"humanwgs_singleton.tertiary_map_file": "s3://<bucket_path>/GRCh38.tertiary_map.v2.hpc.tsv",
"humanwgs_singleton.tertiary_map_file": "s3://<bucket_path>/GRCh38.tertiary_map.v2p0p0-rc2.azure.tsv",
"humanwgs_singleton.backend": "AWS-HealthOmics",
"humanwgs_singleton.container_registry": "String",
"humanwgs_singleton.container_namespace": "String",
Expand Down
12 changes: 12 additions & 0 deletions backends/azure/GRCh38.ref_map.v2p0p0-rc2.azure.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
name GRCh38
fasta /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.fasta
fasta_index /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai
pbsv_splits /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.pbsv_splits.json
pbsv_tandem_repeat_bed /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.trf.bed
trgt_tandem_repeat_bed /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed
hificnv_exclude_bed /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz
hificnv_exclude_bed_index /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz.tbi
hificnv_expected_bed_male /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/expected_cn.hg38.XY.bed
hificnv_expected_bed_female /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/expected_cn.hg38.XX.bed
pharmcat_positions_vcf /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/pharmcat/pharmcat_positions_2.15.0.vcf.bgz
pharmcat_positions_vcf_index /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/pharmcat/pharmcat_positions_2.15.0.vcf.bgz.csi
12 changes: 12 additions & 0 deletions backends/azure/GRCh38.tertiary_map.v2p0p0-rc2.azure.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
slivar_js /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/slivar/slivar-functions.v0.2.8.js
ensembl_gff /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/ensembl.GRCh38.101.reformatted.gff3.gz
lof_lookup /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/slivar/lof_lookup.v2.1.1.txt
clinvar_lookup /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/slivar/clinvar_gene_desc.20240624T165443.txt
slivar_gnotate_files /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/slivar_gnotate/gnomad.hg38.v4.1.custom.v1.zip,/datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/slivar_gnotate/CoLoRSdb.GRCh38.v1.1.0.deepvariant.glnexus.zip
slivar_gnotate_prefixes gnomad,colors
slivar_max_af 0.03
slivar_max_nhomalt 4
slivar_max_ac 4
slivar_min_gq 5
svpack_pop_vcfs /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz,/datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.1.0.pbsv.jasmine.vcf.gz
svpack_pop_vcf_indices /datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz.tbi,/datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.1.0.pbsv.jasmine.vcf.gz.tbi
4 changes: 2 additions & 2 deletions backends/azure/family.azure.inputs.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,9 @@
}
]
},
"humanwgs_family.ref_map_file": "/datasetpbrarediseases/dataset/GRCh38.ref_map.v1.hpc.tsv",
"humanwgs_family.ref_map_file": "/datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38.ref_map.v2p0p0-rc2.azure.tsv",
"humanwgs_family.phenotypes": "String? (optional)",
"humanwgs_family.tertiary_map_file": "/datasetpbrarediseases/dataset/GRCh38.tertiary_map.v2.hpc.tsv",
"humanwgs_family.tertiary_map_file": "/datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38.tertiary_map.v2p0p0-rc2.azure.tsv",
"humanwgs_family.backend": "Azure",
"humanwgs_family.preemptible": "Boolean"
}
4 changes: 2 additions & 2 deletions backends/azure/singleton.azure.inputs.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,9 @@
"humanwgs_singleton.hifi_reads": [
"File"
],
"humanwgs_singleton.ref_map_file": "/datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc1/GRCh38.ref_map.v1.hpc.tsv",
"humanwgs_singleton.ref_map_file": "/datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38.ref_map.v2p0p0-rc2.azure.tsv",
"humanwgs_singleton.phenotypes": "String? (optional)",
"humanwgs_singleton.tertiary_map_file": "/datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc1/GRCh38.tertiary_map.v2.hpc.tsv",
"humanwgs_singleton.tertiary_map_file": "/datasetpbrarediseases/dataset/hifi-wdl-resources-v2.0.0-rc2/GRCh38.tertiary_map.v2p0p0-rc2.azure.tsv",
"humanwgs_singleton.backend": "Azure",
"humanwgs_singleton.preemptible": "Boolean"
}
12 changes: 12 additions & 0 deletions backends/gcp/GRCh38.ref_map.v2p0p0-rc2.gcp.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
name GRCh38
fasta gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.fasta
fasta_index gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai
pbsv_splits gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.pbsv_splits.json
pbsv_tandem_repeat_bed gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.trf.bed
trgt_tandem_repeat_bed gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed
hificnv_exclude_bed gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz
hificnv_exclude_bed_index gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz.tbi
hificnv_expected_bed_male gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/expected_cn.hg38.XY.bed
hificnv_expected_bed_female gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/expected_cn.hg38.XX.bed
pharmcat_positions_vcf gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/pharmcat/pharmcat_positions_2.15.0.vcf.bgz
pharmcat_positions_vcf_index gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/pharmcat/pharmcat_positions_2.15.0.vcf.bgz.csi
12 changes: 12 additions & 0 deletions backends/gcp/GRCh38.tertiary_map.v2p0p0-rc2.gcp.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
slivar_js gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/slivar/slivar-functions.v0.2.8.js
ensembl_gff gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/ensembl.GRCh38.101.reformatted.gff3.gz
lof_lookup gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/slivar/lof_lookup.v2.1.1.txt
clinvar_lookup gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/slivar/clinvar_gene_desc.20240624T165443.txt
slivar_gnotate_files gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/slivar_gnotate/gnomad.hg38.v4.1.custom.v1.zip,gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/slivar_gnotate/CoLoRSdb.GRCh38.v1.1.0.deepvariant.glnexus.zip
slivar_gnotate_prefixes gnomad,colors
slivar_max_af 0.03
slivar_max_nhomalt 4
slivar_max_ac 4
slivar_min_gq 5
svpack_pop_vcfs gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz,gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.1.0.pbsv.jasmine.vcf.gz
svpack_pop_vcf_indices gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz.tbi,gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.1.0.pbsv.jasmine.vcf.gz.tbi
4 changes: 2 additions & 2 deletions backends/gcp/family.gcp.inputs.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,9 @@
}
]
},
"humanwgs_family.ref_map_file": "gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc1/GRCh38.ref_map.v2p0p0-rc1.gcp.tsv",
"humanwgs_family.ref_map_file": "gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38.ref_map.v2p0p0-rc2.gcp.tsv",
"humanwgs_family.phenotypes": "String? (optional)",
"humanwgs_family.tertiary_map_file": "gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc1/GRCh38.tertiary_map.v2p0p0-rc1.gcp.tsv",
"humanwgs_family.tertiary_map_file": "gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38.tertiary_map.v2p0p0-rc2.gcp.tsv",
"humanwgs_family.backend": "GCP",
"humanwgs_family.zones": "String",
"humanwgs_family.preemptible": "Boolean"
Expand Down
4 changes: 2 additions & 2 deletions backends/gcp/singleton.gcp.inputs.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,9 @@
"humanwgs_singleton.hifi_reads": [
"File"
],
"humanwgs_singleton.ref_map_file": "gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc1/GRCh38.ref_map.v2p0p0-rc1.gcp.tsv",
"humanwgs_singleton.ref_map_file": "gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38.ref_map.v2p0p0-rc2.gcp.tsv",
"humanwgs_singleton.phenotypes": "String? (optional)",
"humanwgs_singleton.tertiary_map_file": "gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc1/GRCh38.tertiary_map.v2p0p0-rc1.gcp.tsv",
"humanwgs_singleton.tertiary_map_file": "gs://pacbio-wdl/hifi-wdl-resources-v2.0.0-rc2/GRCh38.tertiary_map.v2p0p0-rc2.gcp.tsv",
"humanwgs_singleton.backend": "GCP",
"humanwgs_singleton.zones": "String",
"humanwgs_singleton.preemptible": "Boolean"
Expand Down
12 changes: 12 additions & 0 deletions backends/hpc/GRCh38.ref_map.v2p0p0-rc2.template.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
name GRCh38
fasta <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.fasta
fasta_index <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai
pbsv_splits <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.pbsv_splits.json
pbsv_tandem_repeat_bed <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/human_GRCh38_no_alt_analysis_set.trf.bed
trgt_tandem_repeat_bed <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed
hificnv_exclude_bed <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz
hificnv_exclude_bed_index <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz.tbi
hificnv_expected_bed_male <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/expected_cn.hg38.XY.bed
hificnv_expected_bed_female <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/hificnv/expected_cn.hg38.XX.bed
pharmcat_positions_vcf <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/pharmcat/pharmcat_positions_2.15.0.vcf.bgz
pharmcat_positions_vcf_index <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/pharmcat/pharmcat_positions_2.15.0.vcf.bgz.csi
12 changes: 12 additions & 0 deletions backends/hpc/GRCh38.tertiary_map.v2p0p0-rc2.template.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
slivar_js <prefix>/hifi-wdl-resources-v2.0.0-rc2/slivar/slivar-functions.v0.2.8.js
ensembl_gff <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/ensembl.GRCh38.101.reformatted.gff3.gz
lof_lookup <prefix>/hifi-wdl-resources-v2.0.0-rc2/slivar/lof_lookup.v2.1.1.txt
clinvar_lookup <prefix>/hifi-wdl-resources-v2.0.0-rc2/slivar/clinvar_gene_desc.20240624T165443.txt
slivar_gnotate_files <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/slivar_gnotate/gnomad.hg38.v4.1.custom.v1.zip,<prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/slivar_gnotate/CoLoRSdb.GRCh38.v1.1.0.deepvariant.glnexus.zip
slivar_gnotate_prefixes gnomad,colors
slivar_max_af 0.03
slivar_max_nhomalt 4
slivar_max_ac 4
slivar_min_gq 5
svpack_pop_vcfs <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz,<prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.1.0.pbsv.jasmine.vcf.gz
svpack_pop_vcf_indices <prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz.tbi,<prefix>/hifi-wdl-resources-v2.0.0-rc2/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.1.0.pbsv.jasmine.vcf.gz.tbi

0 comments on commit 0747310

Please sign in to comment.