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Make manta region bed index required #635

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Feb 2, 2024
Merged

Make manta region bed index required #635

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cb6f070
Make manta region bed index required
VJalili Feb 2, 2024
5aee14d
Add manta_region_bed_index to input templates.
VJalili Feb 2, 2024
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1 change: 1 addition & 0 deletions ...lates/terra_workspaces/cohort_mode/workflow_configurations/GatherSampleEvidence.json.tmpl
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Expand Up @@ -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}",

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1 change: 1 addition & 0 deletions inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl
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Expand Up @@ -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 }}
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1 change: 1 addition & 0 deletions inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl
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Expand Up @@ -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}",
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1 change: 1 addition & 0 deletions inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl
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Expand Up @@ -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 }}
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1 change: 1 addition & 0 deletions inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl
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Expand Up @@ -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 }},
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1 change: 1 addition & 0 deletions inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl
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Expand Up @@ -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 }},
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1 change: 1 addition & 0 deletions inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl
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Expand Up @@ -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 }},
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1 change: 1 addition & 0 deletions ...ts/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl
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Expand Up @@ -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 }},
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1 change: 1 addition & 0 deletions inputs/templates/test/GatherSampleEvidence/GatherSampleEvidence.json.tmpl
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Expand Up @@ -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 }},
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1 change: 1 addition & 0 deletions inputs/templates/test/GatherSampleEvidenceBatch/GatherSampleEvidenceBatch.json.tmpl
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Expand Up @@ -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 }},

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2 changes: 1 addition & 1 deletion wdl/GATKSVPipelineSingleSample.wdl
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Expand Up @@ -103,7 +103,7 @@ workflow GATKSVPipelineSingleSample {

# Manta inputs
File manta_region_bed
File? manta_region_bed_index
File manta_region_bed_index
Float? manta_jobs_per_cpu
Int? manta_mem_gb_per_job

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2 changes: 1 addition & 1 deletion wdl/GatherSampleEvidence.wdl
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Expand Up @@ -55,7 +55,7 @@ workflow GatherSampleEvidence {

# Manta inputs
File manta_region_bed
File? manta_region_bed_index
File manta_region_bed_index
Float? manta_jobs_per_cpu
Int? manta_mem_gb_per_job

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2 changes: 1 addition & 1 deletion wdl/GatherSampleEvidenceBatch.wdl
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Expand Up @@ -33,7 +33,7 @@ workflow GatherSampleEvidenceBatch {

# Manta inputs
File manta_region_bed
File? manta_region_bed_index
File manta_region_bed_index
Float? manta_jobs_per_cpu
Int? manta_mem_gb_per_job

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9 changes: 4 additions & 5 deletions wdl/Manta.wdl
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Expand Up @@ -15,7 +15,7 @@ workflow Manta {
File reference_fasta
File? reference_index
File region_bed
File? region_bed_index
File region_bed_index
Float? jobs_per_cpu
Int? mem_gb_per_job
String manta_docker
Expand All @@ -28,8 +28,8 @@ workflow Manta {
sample_id: "sample name. Outputs will be sample_name + 'manta.vcf.gz' and sample_name + 'manta.vcf.gz.tbi'"
reference_fasta: ".fasta file with reference used to align bam or cram file"
reference_index: "[optional] If omitted, the WDL will look for an index by appending .fai to the .fasta file"
region_bed: "[optional] gzipped bed file with included regions where manta should make SV calls."
region_bed_index: "[optional]If omitted, the WDL will look for an index by appending .tbi to the region_bed file"
region_bed: "gzipped bed file with included regions where manta should make SV calls."
region_bed_index: "A .tbi file for the region_bed file"
jobs_per_cpu: "[optional] number of manta threads, i.e. num_jobs = round(num_cpu * jobs_per_cpu). If omitted, defaults to 1.3."
mem_gb_per_job: "[optional] Memory to request for VM (in GB) = round(num_jobs * mem_gb_per_job). If omitted, defaults to 2."
}
Expand Down Expand Up @@ -63,7 +63,7 @@ task RunManta {
File reference_fasta
File? reference_index
File region_bed
File? region_bed_index
File region_bed_index
Float? jobs_per_cpu
Int? mem_gb_per_job
String manta_docker
Expand All @@ -74,7 +74,6 @@ task RunManta {
String bam_ext = if is_bam then ".bam" else ".cram"
String index_ext = if is_bam then ".bai" else ".crai"
File ref_index = select_first([reference_index, reference_fasta + ".fai"])
File bed_index = select_first([region_bed_index, region_bed + ".tbi"])

# select number of cpus and jobs
Int num_cpu_use = if defined(runtime_attr_override) then select_first([select_first([runtime_attr_override]).cpu_cores, 8]) else 8
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