Add manta_region_bed_index to input templates.

broadinstitute · Feb 2, 2024 · 5aee14d · 5aee14d
1 parent cb6f070
commit 5aee14d
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Showing 10 changed files with 10 additions and 0 deletions.
diff --git a/...lates/terra_workspaces/cohort_mode/workflow_configurations/GatherSampleEvidence.json.tmpl b/...lates/terra_workspaces/cohort_mode/workflow_configurations/GatherSampleEvidence.json.tmpl
@@ -11,6 +11,7 @@
   "GatherSampleEvidence.preprocessed_intervals": "${workspace.preprocessed_intervals}",
 
   "GatherSampleEvidence.manta_region_bed": "${workspace.manta_region_bed}",
+  "GatherSampleEvidence.manta_region_bed_index": "${workspace.manta_region_bed_index}",
   "GatherSampleEvidence.sd_locs_vcf": "${workspace.sd_locs_vcf}",
   "GatherSampleEvidence.melt_standard_vcf_header": "${workspace.melt_standard_vcf_header}",
 

diff --git a/inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl
@@ -32,6 +32,7 @@ external_af_ref_bed	{{ reference_resources.external_af_ref_bed }}
 external_af_ref_bed_prefix	{{ reference_resources.external_af_ref_bed_prefix }}
 genome_file	{{ reference_resources.genome_file }}
 manta_region_bed	{{ reference_resources.manta_region_bed }}
+manta_region_bed_index	{{ reference_resources.manta_region_bed_index }}
 mei_bed	{{ reference_resources.mei_bed }}
 melt_standard_vcf_header	{{ reference_resources.melt_std_vcf_header }}
 noncoding_bed	{{ reference_resources.noncoding_bed }}

diff --git a/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl b/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl
@@ -51,6 +51,7 @@
   "GATKSVPipelineSingleSample.genome_file" : "${workspace.reference_genome_file}",
   "GATKSVPipelineSingleSample.max_ref_panel_carrier_freq": 0.03,
   "GATKSVPipelineSingleSample.manta_region_bed" : "${workspace.reference_manta_region_bed}",
+  "GATKSVPipelineSingleSample.manta_region_bed_index" : "${workspace.reference_manta_region_bed_index}",
   "GATKSVPipelineSingleSample.sd_locs_vcf" : "${workspace.reference_sd_locs_vcf}",
   "GATKSVPipelineSingleSample.reference_dict" : "${workspace.reference_dict}",
   "GATKSVPipelineSingleSample.reference_fasta" : "${workspace.reference_fasta}",

diff --git a/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl b/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl
@@ -53,6 +53,7 @@ reference_external_af_ref_bed	{{ reference_resources.external_af_ref_bed }}
 reference_external_af_ref_bed_prefix	{{ reference_resources.external_af_ref_bed_prefix }}
 reference_genome_file	{{ reference_resources.genome_file }}
 reference_manta_region_bed	{{ reference_resources.manta_region_bed }}
+reference_manta_region_bed_index	{{ reference_resources.manta_region_bed_index }}
 reference_mei_bed	{{ reference_resources.mei_bed }}
 reference_melt_std_vcf_header	{{ reference_resources.melt_std_vcf_header }}
 reference_noncoding_bed	{{ reference_resources.noncoding_bed }}

diff --git a/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl b/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl
@@ -52,6 +52,7 @@
 
   "GATKSVPipelineBatch.GatherSampleEvidenceBatch.reference_version": {{ reference_resources.reference_version | tojson }},
   "GATKSVPipelineBatch.GatherSampleEvidenceBatch.manta_region_bed": {{ reference_resources.manta_region_bed | tojson }},
+  "GATKSVPipelineBatch.GatherSampleEvidenceBatch.manta_region_bed_index": {{ reference_resources.manta_region_bed_index | tojson }},
   "GATKSVPipelineBatch.GatherSampleEvidenceBatch.sd_locs_vcf": {{ reference_resources.sd_locs_vcf | tojson }},
   "GATKSVPipelineBatch.GatherSampleEvidenceBatch.melt_standard_vcf_header": {{ reference_resources.melt_std_vcf_header | tojson }},
   "GATKSVPipelineBatch.GatherSampleEvidenceBatch.wham_include_list_bed_file": {{ reference_resources.wham_include_list_bed_file | tojson }},

diff --git a/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl b/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl
@@ -46,6 +46,7 @@
 
   "GATKSVPipelineBatch.GatherSampleEvidenceBatch.reference_version": {{ reference_resources.reference_version | tojson }},
   "GATKSVPipelineBatch.GatherSampleEvidenceBatch.manta_region_bed": {{ reference_resources.manta_region_bed | tojson }},
+  "GATKSVPipelineBatch.GatherSampleEvidenceBatch.manta_region_bed_index": {{ reference_resources.manta_region_bed_index | tojson }},
   "GATKSVPipelineBatch.GatherSampleEvidenceBatch.sd_locs_vcf": {{ reference_resources.sd_locs_vcf | tojson }},
   "GATKSVPipelineBatch.GatherSampleEvidenceBatch.melt_standard_vcf_header": {{ reference_resources.melt_std_vcf_header | tojson }},
   "GATKSVPipelineBatch.GatherSampleEvidenceBatch.wham_include_list_bed_file": {{ reference_resources.wham_include_list_bed_file | tojson }},

diff --git a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl
@@ -50,6 +50,7 @@
   "GATKSVPipelineSingleSample.genome_file" : {{ reference_resources.genome_file | tojson }},
   "GATKSVPipelineSingleSample.max_ref_panel_carrier_freq": 0.03,
   "GATKSVPipelineSingleSample.manta_region_bed" : {{ reference_resources.manta_region_bed | tojson }},
+  "GATKSVPipelineSingleSample.manta_region_bed_index" : {{ reference_resources.manta_region_bed_index | tojson }},
   "GATKSVPipelineSingleSample.melt_standard_vcf_header": {{ reference_resources.melt_std_vcf_header | tojson }},
   "GATKSVPipelineSingleSample.sd_locs_vcf": {{ reference_resources.sd_locs_vcf | tojson }},
   "GATKSVPipelineSingleSample.reference_dict" : {{ reference_resources.reference_dict | tojson }},

diff --git a/...ts/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl b/...ts/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl
@@ -53,6 +53,7 @@
   "GATKSVPipelineSingleSample.genome_file" : {{ reference_resources.genome_file | tojson }},
   "GATKSVPipelineSingleSample.max_ref_panel_carrier_freq": 0.03,
   "GATKSVPipelineSingleSample.manta_region_bed" : {{ reference_resources.manta_region_bed | tojson }},
+  "GATKSVPipelineSingleSample.manta_region_bed_index" : {{ reference_resources.manta_region_bed_index | tojson }},
   "GATKSVPipelineSingleSample.sd_locs_vcf" : {{ reference_resources.sd_locs_vcf | tojson }},
   "GATKSVPipelineSingleSample.reference_dict" : {{ reference_resources.reference_dict | tojson }},
   "GATKSVPipelineSingleSample.reference_fasta" : {{ reference_resources.reference_fasta | tojson }},

diff --git a/inputs/templates/test/GatherSampleEvidence/GatherSampleEvidence.json.tmpl b/inputs/templates/test/GatherSampleEvidence/GatherSampleEvidence.json.tmpl
@@ -14,6 +14,7 @@
 
   "GatherSampleEvidence.preprocessed_intervals": {{ reference_resources.preprocessed_intervals | tojson }},
   "GatherSampleEvidence.manta_region_bed": {{ reference_resources.manta_region_bed | tojson }},
+  "GatherSampleEvidence.manta_region_bed_index": {{ reference_resources.manta_region_bed_index | tojson }},
   "GatherSampleEvidence.sd_locs_vcf": {{ reference_resources.sd_locs_vcf | tojson }},
   "GatherSampleEvidence.melt_standard_vcf_header": {{ reference_resources.melt_std_vcf_header | tojson }},
   "GatherSampleEvidence.wham_include_list_bed_file": {{ reference_resources.wham_include_list_bed_file | tojson }},

diff --git a/inputs/templates/test/GatherSampleEvidenceBatch/GatherSampleEvidenceBatch.json.tmpl b/inputs/templates/test/GatherSampleEvidenceBatch/GatherSampleEvidenceBatch.json.tmpl
@@ -11,6 +11,7 @@
   "GatherSampleEvidenceBatch.preprocessed_intervals": {{ reference_resources.preprocessed_intervals | tojson }},
 
   "GatherSampleEvidenceBatch.manta_region_bed": {{ reference_resources.manta_region_bed | tojson }},
+  "GatherSampleEvidenceBatch.manta_region_bed_index": {{ reference_resources.manta_region_bed_index | tojson }},
   "GatherSampleEvidenceBatch.sd_locs_vcf": {{ reference_resources.sd_locs_vcf | tojson }},
   "GatherSampleEvidenceBatch.melt_standard_vcf_header": {{ reference_resources.melt_std_vcf_header | tojson }},