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@williamrowell
williamrowell committed Feb 4, 2025
1 parent ecdbf3e commit fce5c23
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Showing 9 changed files with 256 additions and 241 deletions.
293 changes: 171 additions & 122 deletions wdl-ci.config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -535,11 +535,11 @@
},
"sv_stats": {
"key": "sv_stats",
"digest": "35gn2cqouobao6vacrqbi67zhkh6nmyn",
"digest": "foqixa2ryrx7e64ymqylurlfad7gpdpi",
"tests": [
{
"inputs": {
"vcf": "${resources_file_path}/sv_stats/HG002.GRCh38.pbsv.phased.vcf.gz",
"vcf": "${resources_file_path}/sawfish_call/output/HG002/HG002.GRCh38.structural_variants.vcf.gz",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
Expand All @@ -550,13 +550,13 @@
]
},
"stat_sv_DEL_count": {
"value": "19",
"value": "17",
"test_tasks": [
"compare_string"
]
},
"stat_sv_INS_count": {
"value": "37",
"value": "46",
"test_tasks": [
"compare_string"
]
Expand All @@ -568,7 +568,13 @@
]
},
"stat_sv_BND_count": {
"value": "0",
"value": "2",
"test_tasks": [
"compare_string"
]
},
"stat_sv_INVBND_count": {
"value": "4",
"test_tasks": [
"compare_string"
]
Expand Down Expand Up @@ -964,7 +970,7 @@
"tasks": {
"merge_bam_stats": {
"key": "merge_bam_stats",
"digest": "fgbffrsqd32kov6i43cidmt2u5lgvn7g",
"digest": "mjd6zpbxtabbulmq3kwhcx4cnubxaf74",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -1515,120 +1521,6 @@
}
}
},
"workflows/wdl-common/wdl/tasks/pbsv.wdl": {
"key": "workflows/wdl-common/wdl/tasks/pbsv.wdl",
"name": "",
"description": "",
"tasks": {
"pbsv_discover": {
"key": "pbsv_discover",
"digest": "mcdiubcggjbwaweaciocgrnypvqn5tnb",
"tests": [
{
"inputs": {
"aligned_bam": "${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.bam",
"aligned_bam_index": "${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.bam.bai",
"trf_bed": "${datasets_file_path}/GRCh38/human_GRCh38_no_alt_analysis_set.trf.bed",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"svsig": {
"value": "${resources_file_path}/pbsv_discover/HG002.GRCh38.chr6_10000000_20000000.svsig.gz",
"test_tasks": [
"compare_file_basename",
"check_gzip",
"check_empty_lines"
]
}
}
}
]
},
"pbsv_call": {
"key": "pbsv_call",
"digest": "2rhytrhz52jofq7lv42akixzl55wa3lk",
"tests": [
{
"inputs": {
"sample_id": "HG002",
"svsigs": [
"${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.svsig.gz"
],
"ref_fasta": "${ref_fasta}",
"ref_index": "${ref_index}",
"ref_name": "${ref_name}",
"shard_index": 5,
"regions": [
"chr6"
],
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"vcf": {
"value": "${resources_file_path}/pbsv_call/singleton/HG002.GRCh38.5.pbsv.vcf.gz",
"test_tasks": [
"compare_file_basename",
"vcftools_validator",
"check_gzip"
]
}
}
},
{
"inputs": {
"sample_id": "HG002",
"svsigs": [
"${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.svsig.gz"
],
"ref_fasta": "${ref_fasta}",
"ref_index": "${ref_index}",
"ref_name": "${ref_name}",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"vcf": {
"value": "${resources_file_path}/pbsv_call/singleton_no_shard/HG002.GRCh38.pbsv.vcf.gz",
"test_tasks": [
"compare_file_basename",
"vcftools_validator",
"check_gzip"
]
}
}
},
{
"inputs": {
"sample_id": "HG002-trio",
"svsigs": [
"${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.svsig.gz",
"${resources_file_path}/inputs/HG003.GRCh38.chr6_10000000_20000000.svsig.gz",
"${resources_file_path}/inputs/HG004.GRCh38.chr6_10000000_20000000.svsig.gz"
],
"sample_count": 3,
"ref_fasta": "${ref_fasta}",
"ref_index": "${ref_index}",
"ref_name": "${ref_name}",
"shard_index": 5,
"regions": [
"chr6"
],
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"vcf": {
"value": "${resources_file_path}/pbsv_call/trio/HG002-trio.GRCh38.5.pbsv.vcf.gz",
"test_tasks": [
"compare_file_basename",
"vcftools_validator",
"check_gzip"
]
}
}
}
]
}
}
},
"workflows/wdl-common/wdl/tasks/samtools.wdl": {
"key": "workflows/wdl-common/wdl/tasks/samtools.wdl",
"name": "",
Expand Down Expand Up @@ -1678,7 +1570,7 @@
"tasks": {
"trgt": {
"key": "trgt",
"digest": "rpcfzfr5reqxv7jbtfncu6etivzxvgs2",
"digest": "6i7troewkutvnmy6oft2vkgeltp2jh3z",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -1767,7 +1659,7 @@
},
"trgt_merge": {
"key": "trgt_merge",
"digest": "cmdcqkqrcfpn2eoczxfwhs6zqhalzdtt",
"digest": "ljvpgmkt7sfdwpm64dqllrphd23ols56",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -2461,6 +2353,163 @@
]
}
}
},
"workflows/wdl-common/wdl/tasks/sawfish.wdl": {
"key": "workflows/wdl-common/wdl/tasks/sawfish.wdl",
"name": "",
"description": "",
"tasks": {
"sawfish_discover": {
"key": "sawfish_discover",
"digest": "eh67skuq3swjgkbrinqhzfxf2wfea2hp",
"tests": [
{
"inputs": {
"sex": "MALE",
"aligned_bam": "${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.bam",
"aligned_bam_index": "${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.bam.bai",
"ref_fasta": "${ref_fasta}",
"ref_index": "${ref_index}",
"expected_male_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/expected_cn.hg38.XY.bed",
"expected_female_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/expected_cn.hg38.XX.bed",
"out_prefix": "HG002.GRCh38",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"discover_tar": {
"value": "${resources_file_path}/sawfish_discover/output/HG002/HG002.GRCh38.tar",
"test_tasks": [
"compare_file_basename"
]
}
}
},
{
"inputs": {
"sex": "MALE",
"aligned_bam": "${resources_file_path}/inputs/HG003.GRCh38.chr6_10000000_20000000.bam",
"aligned_bam_index": "${resources_file_path}/inputs/HG003.GRCh38.chr6_10000000_20000000.bam.bai",
"ref_fasta": "${ref_fasta}",
"ref_index": "${ref_index}",
"expected_male_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/expected_cn.hg38.XY.bed",
"expected_female_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/expected_cn.hg38.XX.bed",
"out_prefix": "HG003.GRCh38",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"discover_tar": {
"value": "${resources_file_path}/sawfish_discover/output/HG003/HG003.GRCh38.tar",
"test_tasks": [
"compare_file_basename"
]
}
}
},
{
"inputs": {
"aligned_bam": "${resources_file_path}/inputs/HG004.GRCh38.chr6_10000000_20000000.bam",
"aligned_bam_index": "${resources_file_path}/inputs/HG004.GRCh38.chr6_10000000_20000000.bam.bai",
"ref_fasta": "${ref_fasta}",
"ref_index": "${ref_index}",
"expected_male_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/expected_cn.hg38.XY.bed",
"expected_female_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/expected_cn.hg38.XX.bed",
"out_prefix": "HG004.GRCh38",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"discover_tar": {
"value": "${resources_file_path}/sawfish_discover/output/HG004/HG004.GRCh38.tar",
"test_tasks": [
"compare_file_basename"
]
}
}
}
]
},
"sawfish_call": {
"key": "sawfish_call",
"digest": "gcc2gfurgryq2ziqgyfgxc5a2k3dtkyo",
"tests": [
{
"inputs": {
"discover_tars": [
"${resources_file_path}/sawfish_call/input/HG002.GRCh38.tar"
],
"aligned_bams": [
"${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.bam"
],
"aligned_bam_indices": [
"${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.bam.bai"
],
"ref_fasta": "${ref_fasta}",
"ref_index": "${ref_index}",
"ref_name": "${ref_name}",
"out_prefix": "HG002.GRCh38.structural_variants",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"vcf": {
"value": "${resources_file_path}/sawfish_call/output/HG002/HG002.GRCh38.structural_variants.vcf.gz",
"test_tasks": [
"compare_file_basename",
"check_gzip",
"vcftools_validator"
]
},
"supporting_reads": {
"value": "${resources_file_path}/sawfish_call/output/HG002/HG002.GRCh38.structural_variants.supporting_reads.json.gz",
"test_tasks": [
"compare_file_basename",
"check_gzip"
]
}
}
},
{
"inputs": {
"discover_tars": [
"${resources_file_path}/sawfish_call/input/HG002.GRCh38.tar",
"${resources_file_path}/sawfish_call/input/HG003.GRCh38.tar",
"${resources_file_path}/sawfish_call/input/HG004.GRCh38.tar"
],
"aligned_bams": [
"${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.bam",
"${resources_file_path}/inputs/HG003.GRCh38.chr6_10000000_20000000.bam",
"${resources_file_path}/inputs/HG004.GRCh38.chr6_10000000_20000000.bam"
],
"aligned_bam_indices": [
"${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.bam.bai",
"${resources_file_path}/inputs/HG003.GRCh38.chr6_10000000_20000000.bam.bai",
"${resources_file_path}/inputs/HG004.GRCh38.chr6_10000000_20000000.bam.bai"
],
"ref_fasta": "${ref_fasta}",
"ref_index": "${ref_index}",
"ref_name": "${ref_name}",
"out_prefix": "HG002-trio.joint.GRCh38.structural_variants",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"vcf": {
"value": "${resources_file_path}/sawfish_call/output/HG002-trio/HG002-trio.joint.GRCh38.structural_variants.vcf.gz",
"test_tasks": [
"compare_file_basename",
"check_gzip",
"vcftools_validator"
]
},
"supporting_reads": {
"value": "${resources_file_path}/sawfish_call/output/HG002-trio/HG002-trio.joint.GRCh38.structural_variants.supporting_reads.json.gz",
"test_tasks": [
"compare_file_basename",
"check_gzip"
]
}
}
}
]
}
}
}
},
"engines": {
Expand Down
11 changes: 6 additions & 5 deletions workflows/downstream/downstream.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -191,11 +191,12 @@ workflow downstream {
File indel_distribution_plot = bcftools_stats_roh_small_variants.indel_distribution_plot

# sv stats
String stat_sv_DUP_count = sv_stats.stat_sv_DUP_count
String stat_sv_DEL_count = sv_stats.stat_sv_DEL_count
String stat_sv_INS_count = sv_stats.stat_sv_INS_count
String stat_sv_INV_count = sv_stats.stat_sv_INV_count
String stat_sv_BND_count = sv_stats.stat_sv_BND_count
String stat_sv_DUP_count = sv_stats.stat_sv_DUP_count
String stat_sv_DEL_count = sv_stats.stat_sv_DEL_count
String stat_sv_INS_count = sv_stats.stat_sv_INS_count
String stat_sv_INV_count = sv_stats.stat_sv_INV_count
String stat_sv_INVBND_count = sv_stats.stat_sv_INVBND_count
String stat_sv_BND_count = sv_stats.stat_sv_BND_count

# cpg_pileup outputs
File? cpg_combined_bed = cpg_pileup.combined_bed
Expand Down
1 change: 0 additions & 1 deletion workflows/family.inputs.json
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,6 @@
"humanwgs_family.pharmcat_min_coverage": "Int (optional, default = 10)",
"humanwgs_family.tertiary_map_file": "File? (optional)",
"humanwgs_family.glnexus_mem_gb": "Int? (optional)",
"humanwgs_family.pbsv_call_mem_gb": "Int? (optional)",
"humanwgs_family.gpu": "Boolean (optional, default = false)",
"humanwgs_family.backend": "String",
"humanwgs_family.zones": "String? (optional)",
Expand Down
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