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Sharded AnnotateVcf workflow #566

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merged 26 commits into from
Aug 4, 2023
Merged

Sharded AnnotateVcf workflow #566

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3619cf4
carry over Xuefang's changes to AnnotateVcf from gnomAD v3
epiercehoffman Dec 15, 2022
e8562c9
remove gnomAD-specific END fix and make contigs list a file
epiercehoffman Dec 16, 2022
d46986f
make hail docker optional
epiercehoffman Dec 16, 2022
95fc026
make prune vcf samples step & input optional
epiercehoffman Dec 16, 2022
b0fa6fd
create tabix index if not in expected location in svannotate
epiercehoffman Jan 6, 2023
09b695b
samples list input to compute_AFs.py
epiercehoffman Jan 26, 2023
d053a58
update WDLs and docker with samples list for compute afs
epiercehoffman Jan 27, 2023
1a583be
keep external af annotation, update json templates
epiercehoffman May 2, 2023
3e65184
shard by contig if inputs are not already
epiercehoffman May 8, 2023
087364d
use latest ScatterVcf. also reverted sample list for compute AFs duri…
epiercehoffman May 8, 2023
148319c
womtool validation
epiercehoffman May 8, 2023
fc16f00
cleanup
epiercehoffman May 8, 2023
f87ea28
more cleanup
epiercehoffman May 8, 2023
6e51b6d
whitespace
epiercehoffman May 8, 2023
b92591b
merge output to same level as input
epiercehoffman May 8, 2023
6f4f350
pass index to scatter
epiercehoffman Jul 6, 2023
28a0a93
annotate ext af per shard
epiercehoffman Jul 6, 2023
0880aef
remove AnnotateExternalAF.wdl
epiercehoffman Jul 7, 2023
d94df6d
make index optional
epiercehoffman Jul 10, 2023
dcc341d
remove sharded_by_contig input from jsons
epiercehoffman Jul 10, 2023
b8ccd52
womtool validation
epiercehoffman Jul 10, 2023
578af9e
single vcf input. require index & infer path
epiercehoffman Jul 27, 2023
b107c05
don't generate index if not present in ScatterVcf
epiercehoffman Jul 27, 2023
e1bb41c
clean up runtime attrs
epiercehoffman Jul 27, 2023
d52ac3d
move PruneAndAddVafs tasks to ShardedAnnotateVcf
epiercehoffman Jul 27, 2023
ae48efa
remove PruneAndAddVafs.wdl
epiercehoffman Jul 27, 2023
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9 changes: 4 additions & 5 deletions ...es/terra_workspaces/cohort_mode/workflow_configurations/AnnotateVcf.SingleBatch.json.tmpl
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@@ -1,6 +1,6 @@
{
"AnnotateVcf.vcf" : "${this.cleaned_vcf}",
"AnnotateVcf.vcf_idx" : "${this.cleaned_vcf_index}",
"AnnotateVcf.vcf_list" : "${this.cleaned_vcf}",
"AnnotateVcf.vcf_idx_list" : "${this.cleaned_vcf_index}",
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"AnnotateVcf.protein_coding_gtf" : "${workspace.protein_coding_gtf}",
"AnnotateVcf.noncoding_bed" : "${workspace.noncoding_bed}",
Expand All @@ -12,10 +12,9 @@
"AnnotateVcf.contig_list" : "${workspace.primary_contigs_list}",
"AnnotateVcf.ped_file": "${workspace.cohort_ped_file}",
"AnnotateVcf.sv_per_shard" : "5000",
"AnnotateVcf.max_shards_per_chrom_step1" : 200,
"AnnotateVcf.min_records_per_shard_step1" : 5000,

"AnnotateVcf.prefix" : "${this.sample_set_id}",
"AnnotateVcf.prefix_list" : "${this.sample_set_id}",
"AnnotateVcf.use_hail": "false",

"AnnotateVcf.gatk_docker" : "${workspace.gatk_docker}",
"AnnotateVcf.sv_base_mini_docker" : "${workspace.sv_base_mini_docker}",
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11 changes: 5 additions & 6 deletions inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/AnnotateVcf.json.tmpl
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"AnnotateVcf.vcf" : "${this.cleaned_vcf}",
"AnnotateVcf.vcf_idx" : "${this.cleaned_vcf_index}",
"AnnotateVcf.vcf_list" : "${this.cleaned_vcf}",
"AnnotateVcf.vcf_idx_list" : "${this.cleaned_vcf_index}",
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"AnnotateVcf.protein_coding_gtf" : "${workspace.protein_coding_gtf}",
"AnnotateVcf.noncoding_bed" : "${workspace.noncoding_bed}",
Expand All @@ -12,10 +12,9 @@
"AnnotateVcf.contig_list" : "${workspace.primary_contigs_list}",
"AnnotateVcf.ped_file": "${workspace.cohort_ped_file}",
"AnnotateVcf.sv_per_shard" : "5000",
"AnnotateVcf.max_shards_per_chrom_step1" : 200,
"AnnotateVcf.min_records_per_shard_step1" : 5000,

"AnnotateVcf.prefix" : "${this.sample_set_set_id}",

"AnnotateVcf.prefix_list" : "${this.sample_set_set_id}",
"AnnotateVcf.use_hail": "false",

"AnnotateVcf.gatk_docker" : "${workspace.gatk_docker}",
"AnnotateVcf.sv_base_mini_docker" : "${workspace.sv_base_mini_docker}",
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2 changes: 0 additions & 2 deletions inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl
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Expand Up @@ -102,8 +102,6 @@
"GATKSVPipelineSingleSample.external_af_population" : {{ reference_resources.external_af_population | tojson }},

"GATKSVPipelineSingleSample.annotation_sv_per_shard" : "5000",
"GATKSVPipelineSingleSample.annotation_max_shards_per_chrom_step1" : 200,
"GATKSVPipelineSingleSample.annotation_min_records_per_shard_step1" : 5000,

"GATKSVPipelineSingleSample.ref_samples_list" : "${workspace.ref_panel_samples_list}",
"GATKSVPipelineSingleSample.ref_std_manta_vcf_tar" : "${workspace.ref_panel_std_manta_vcf_tar}",
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9 changes: 4 additions & 5 deletions inputs/templates/test/AnnotateVcf/AnnotateVcf.json.tmpl
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@@ -1,6 +1,6 @@
{
"AnnotateVcf.vcf" : {{ test_batch.clean_vcf | tojson }},
"AnnotateVcf.vcf_idx" : {{ test_batch.clean_vcf_index | tojson }},
"AnnotateVcf.vcf_list" : [ {{ test_batch.clean_vcf | tojson }} ],
"AnnotateVcf.vcf_idx_list" : [{{ test_batch.clean_vcf_index | tojson }}],

"AnnotateVcf.protein_coding_gtf" : {{ reference_resources.protein_coding_gtf | tojson }},
"AnnotateVcf.noncoding_bed" : {{ reference_resources.noncoding_bed | tojson }},
Expand All @@ -12,10 +12,9 @@
"AnnotateVcf.contig_list" : {{ reference_resources.primary_contigs_list | tojson }},
"AnnotateVcf.ped_file": {{ test_batch.ped_file | tojson }},
"AnnotateVcf.sv_per_shard" : "5000",
"AnnotateVcf.max_shards_per_chrom_step1" : 200,
"AnnotateVcf.min_records_per_shard_step1" : 5000,

"AnnotateVcf.prefix" : {{ test_batch.name | tojson }},
"AnnotateVcf.prefix_list" : [{{ test_batch.name | tojson }}],
"AnnotateVcf.use_hail": "false",

"AnnotateVcf.gatk_docker":{{ dockers.gatk_docker | tojson }},
"AnnotateVcf.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }},
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2 changes: 0 additions & 2 deletions inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl
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Expand Up @@ -102,8 +102,6 @@
"GATKSVPipelineSingleSample.external_af_population" : {{ reference_resources.external_af_population | tojson }},

"GATKSVPipelineSingleSample.annotation_sv_per_shard" : "5000",
"GATKSVPipelineSingleSample.annotation_max_shards_per_chrom_step1" : 200,
"GATKSVPipelineSingleSample.annotation_min_records_per_shard_step1" : 5000,

"GATKSVPipelineSingleSample.ref_samples_list" : {{ ref_panel.samples_list | tojson }},
"GATKSVPipelineSingleSample.ref_std_manta_vcf_tar" : {{ ref_panel.std_manta_vcf_tar | tojson }},
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2 changes: 0 additions & 2 deletions ...ts/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl
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Expand Up @@ -104,8 +104,6 @@
"GATKSVPipelineSingleSample.external_af_population" : {{ reference_resources.external_af_population | tojson }},

"GATKSVPipelineSingleSample.annotation_sv_per_shard" : "5000",
"GATKSVPipelineSingleSample.annotation_max_shards_per_chrom_step1" : 200,
"GATKSVPipelineSingleSample.annotation_min_records_per_shard_step1" : 5000,

"GATKSVPipelineSingleSample.ref_samples_list" : {{ ref_panel.samples_list | tojson }},
"GATKSVPipelineSingleSample.ref_std_manta_vcf_tar" : {{ ref_panel.std_manta_vcf_tar | tojson }},
Expand Down
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