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wdl-ci.config.json
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{
"workflows": {
"workflows/main.wdl": {
"key": "workflows/main.wdl",
"name": "",
"description": "",
"tasks": {}
},
"workflows/wdl-common/wdl/structs.wdl": {
"key": "workflows/wdl-common/wdl/structs.wdl",
"name": "",
"description": "",
"tasks": {}
},
"workflows/wdl-common/wdl/tasks/bcftools_stats.wdl": {
"key": "workflows/wdl-common/wdl/tasks/bcftools_stats.wdl",
"name": "",
"description": "",
"tasks": {
"bcftools_stats": {
"key": "bcftools_stats",
"digest": "cu73ojtpnhesxaa2jh7a7l23vlieds3i",
"tests": []
}
}
},
"workflows/wdl-common/wdl/tasks/zip_index_vcf.wdl": {
"key": "workflows/wdl-common/wdl/tasks/zip_index_vcf.wdl",
"name": "",
"description": "",
"tasks": {
"zip_index_vcf": {
"key": "zip_index_vcf",
"digest": "cflenxzb6uj2ujfv4pkllo3vztdkev45",
"tests": []
}
}
},
"workflows/wdl-common/wdl/tasks/samtools_fasta.wdl": {
"key": "workflows/wdl-common/wdl/tasks/samtools_fasta.wdl",
"name": "",
"description": "",
"tasks": {
"samtools_fasta": {
"key": "samtools_fasta",
"digest": "x336uu76d5c6nzls2vgntvoqrnhex5q4",
"tests": [
{
"inputs": {
"bam": "${input_file_path}/small_HG005/m64017_200723_190224.hifi_reads.bam",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"reads_fasta": {
"value": "${resources_file_path}/m64017_200723_190224.hifi_reads.fasta",
"test_tasks": [
"calculate_md5sum",
"compare_file_basename",
"check_empty_lines",
"fasta_validator"
]
}
}
}
]
}
}
},
"workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl": {
"key": "workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl",
"name": "",
"description": "",
"tasks": {}
},
"workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl": {
"key": "workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl",
"name": "",
"description": "",
"tasks": {
"parse_families": {
"key": "parse_families",
"digest": "rsrm6ovjkccljzmidg7yuioyusx3pt2r",
"tests": [
{
"inputs": {
"cohort_json": "${resources_file_path}/cohort.json",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"families_json": {
"value": "${resources_file_path}/families.json",
"test_tasks": [
"calculate_md5sum",
"compare_file_basename",
"check_json"
]
}
}
}
]
},
"yak_count": {
"key": "yak_count",
"digest": "i4jt54vu25mhikalp47febetx7mn6xmo",
"tests": [
{
"inputs": {
"sample_id": "HG007",
"reads_fastas": [
"${resources_file_path}/m64017_191216_194629.hifi_reads.fasta",
"${resources_file_path}/m64017_191218_164535.hifi_reads.fasta",
"${resources_file_path}/m64017_191219_225837.hifi_reads.fasta",
"${resources_file_path}/m64017_191221_052416.hifi_reads.fasta",
"${resources_file_path}/m64017_200108_232219.hifi_reads.fasta",
"${resources_file_path}/m64017_200112_090459.hifi_reads.fasta"
],
"yak_params": "-b37",
"mem_gb": 70,
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"yak": {
"value": "${resources_file_path}/HG007.yak",
"test_tasks": [
"calculate_md5sum",
"compare_file_basename"
]
}
}
}
]
}
}
},
"workflows/assemble_genome/assemble_genome.wdl": {
"key": "workflows/assemble_genome/assemble_genome.wdl",
"name": "",
"description": "",
"tasks": {
"hifiasm_assemble": {
"key": "hifiasm_assemble",
"digest": "uc6632gg3jp67k3sz6yqwrzc6y3x6c4l",
"tests": [
{
"inputs": {
"sample_id": "HG005",
"reads_fastas": [
"${resources_file_path}/m64017_200723_190224.hifi_reads.fasta",
"${resources_file_path}/m64017_200730_190124.hifi_reads.fasta",
"${resources_file_path}/m64017_200801_011415.hifi_reads.fasta",
"${resources_file_path}/m64017_200802_073944.hifi_reads.fasta",
"${resources_file_path}/m64109_200304_195708.hifi_reads.fasta",
"${resources_file_path}/m64109_200309_192110.hifi_reads.fasta",
"${resources_file_path}/m64109_200311_013444.hifi_reads.fasta"
],
"runtime_attributes": "${on_demand_runtime_attributes}"
},
"output_tests": {
"assembly_hap_gfas": {
"value": [
"${resources_file_path}/HG005.asm.bp.hap1.p_ctg.gfa",
"${resources_file_path}/HG005.asm.bp.hap2.p_ctg.gfa"
],
"test_tasks": [
"calculate_md5sum",
"compare_file_basename",
"check_empty_lines"
]
},
"assembly_noseq_gfas": {
"value": [
"${resources_file_path}/HG005.asm.bp.hap1.p_ctg.noseq.gfa",
"${resources_file_path}/HG005.asm.bp.hap2.p_ctg.noseq.gfa"
],
"test_tasks": [
"calculate_md5sum",
"compare_file_basename",
"check_empty_lines"
]
},
"assembly_lowQ_beds": {
"value": [
"${resources_file_path}/HG005.asm.bp.hap1.p_ctg.lowQ.bed",
"${resources_file_path}/HG005.asm.bp.hap2.p_ctg.lowQ.bed"
],
"test_tasks": [
"calculate_md5sum",
"compare_file_basename",
"check_tab_delimited",
"count_columns"
]
}
}
}
]
},
"gfa2fa": {
"key": "gfa2fa",
"digest": "r2xbqxqkae5owmzwkmvfk6atpdiu75vf",
"tests": [
{
"inputs": {
"gfa": "${resources_file_path}/HG005.asm.bp.hap1.p_ctg.gfa",
"reference_index": "${datasets_file_path}/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"zipped_fasta": {
"value": "${resources_file_path}/HG005.asm.bp.hap1.p_ctg.fasta.gz",
"test_tasks": [
"compare_file_basename",
"check_gzip",
"check_empty_lines",
"fasta_validator"
]
},
"assembly_stats": {
"value": "${resources_file_path}/HG005.asm.bp.hap1.p_ctg.fasta.stats.txt",
"test_tasks": [
"compare_file_basename",
"check_tab_delimited",
"check_empty_lines"
]
}
}
}
]
},
"align_hifiasm": {
"key": "align_hifiasm",
"digest": "ib3l4i6tdenf5sa3s54yzxfraxhk5u73",
"tests": [
{
"inputs": {
"sample_id": "HG005",
"query_sequences": "${resources_file_path}/HG005.asm.bp.hap1.p_ctg.fasta.gz",
"reference": "${datasets_file_path}/GRCh38/human_GRCh38_no_alt_analysis_set.fasta",
"reference_name": "GRCh38",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"asm_bam": {
"value": "${resources_file_path}/HG005.hap1.asm.GRCh38.bam",
"test_tasks": [
"compare_file_basename",
"samtools_quickcheck",
"check_coordinate_sorted_alignment"
]
}
}
}
]
},
"merge_haps": {
"key": "merge_haps",
"digest": "",
"tests": []
}
}
},
"workflows/de_novo_assembly_sample/de_novo_assembly_sample.wdl": {
"key": "workflows/de_novo_assembly_sample/de_novo_assembly_sample.wdl",
"name": "",
"description": "",
"tasks": {
"htsbox": {
"key": "htsbox",
"digest": "wzaxerbnwe327lejeyudsposw4ywor7t",
"tests": [
{
"inputs": {
"bam": "${resources_file_path}/HG005.asm.GRCh38.bam",
"bam_index": "${resources_file_path}/HG005.asm.GRCh38.bam.bai",
"reference": "${datasets_file_path}/GRCh38/human_GRCh38_no_alt_analysis_set.fasta",
"runtime_attributes": "${default_runtime_attributes}"
},
"output_tests": {
"htsbox_vcf": {
"value": "${resources_file_path}/HG005.asm.GRCh38.htsbox.vcf",
"test_tasks": [
"compare_file_basename",
"vcftools_validator"
]
}
}
}
]
},
"paftools": {
"key": "paftools",
"digest": "",
"tests": []
}
}
},
"workflows/assembly_structs.wdl": {
"key": "workflows/assembly_structs.wdl",
"name": "",
"description": "",
"tasks": {}
},
"workflows/wdl-common/wdl/tasks/glnexus.wdl": {
"key": "workflows/wdl-common/wdl/tasks/glnexus.wdl",
"name": "",
"description": "",
"tasks": {
"glnexus": {
"key": "glnexus",
"digest": "",
"tests": []
}
}
},
"workflows/wdl-common/wdl/tasks/mosdepth.wdl": {
"key": "workflows/wdl-common/wdl/tasks/mosdepth.wdl",
"name": "",
"description": "",
"tasks": {
"mosdepth": {
"key": "mosdepth",
"digest": "",
"tests": []
}
}
},
"workflows/wdl-common/wdl/tasks/pbsv_call.wdl": {
"key": "workflows/wdl-common/wdl/tasks/pbsv_call.wdl",
"name": "",
"description": "",
"tasks": {
"pbsv_call": {
"key": "pbsv_call",
"digest": "",
"tests": []
}
}
},
"workflows/wdl-common/wdl/tasks/pbsv_discover.wdl": {
"key": "workflows/wdl-common/wdl/tasks/pbsv_discover.wdl",
"name": "",
"description": "",
"tasks": {
"pbsv_discover": {
"key": "pbsv_discover",
"digest": "",
"tests": []
}
}
},
"workflows/wdl-common/wdl/tasks/whatshap_haplotag.wdl": {
"key": "workflows/wdl-common/wdl/tasks/whatshap_haplotag.wdl",
"name": "",
"description": "",
"tasks": {
"whatshap_haplotag": {
"key": "whatshap_haplotag",
"digest": "",
"tests": []
}
}
},
"workflows/wdl-common/wdl/tasks/whatshap_phase.wdl": {
"key": "workflows/wdl-common/wdl/tasks/whatshap_phase.wdl",
"name": "",
"description": "",
"tasks": {
"whatshap_phase": {
"key": "whatshap_phase",
"digest": "",
"tests": []
}
}
},
"workflows/wdl-common/wdl/tasks/whatshap_stats.wdl": {
"key": "workflows/wdl-common/wdl/tasks/whatshap_stats.wdl",
"name": "",
"description": "",
"tasks": {
"whatshap_stats": {
"key": "whatshap_stats",
"digest": "",
"tests": []
}
}
},
"workflows/wdl-common/wdl/workflows/deepvariant/deepvariant.wdl": {
"key": "workflows/wdl-common/wdl/workflows/deepvariant/deepvariant.wdl",
"name": "",
"description": "",
"tasks": {
"deepvariant_make_examples": {
"key": "deepvariant_make_examples",
"digest": "",
"tests": []
},
"deepvariant_call_variants": {
"key": "deepvariant_call_variants",
"digest": "",
"tests": []
},
"deepvariant_postprocess_variants": {
"key": "deepvariant_postprocess_variants",
"digest": "",
"tests": []
}
}
},
"workflows/wdl-common/wdl/workflows/phase_vcf/phase_vcf.wdl": {
"key": "workflows/wdl-common/wdl/workflows/phase_vcf/phase_vcf.wdl",
"name": "",
"description": "",
"tasks": {
"split_vcf": {
"key": "split_vcf",
"digest": "",
"tests": []
},
"bcftools_concat": {
"key": "bcftools_concat",
"digest": "",
"tests": []
}
}
},
"workflows/wdl-common/wdl/workflows/hiphase/hiphase.wdl": {
"key": "workflows/wdl-common/wdl/workflows/hiphase/hiphase.wdl",
"name": "",
"description": "",
"tasks": {
"run_hiphase": {
"key": "run_hiphase",
"digest": "",
"tests": []
}
}
},
"workflows/wdl-common/wdl/workflows/pharmcat/pharmcat.wdl": {
"key": "workflows/wdl-common/wdl/workflows/pharmcat/pharmcat.wdl",
"name": "",
"description": "",
"tasks": {
"pangu_cyp2d6": {
"key": "pangu_cyp2d6",
"digest": "",
"tests": []
},
"pharmcat_preprocess": {
"key": "pharmcat_preprocess",
"digest": "",
"tests": []
},
"filter_preprocessed_vcf": {
"key": "filter_preprocessed_vcf",
"digest": "",
"tests": []
},
"run_pharmcat": {
"key": "run_pharmcat",
"digest": "",
"tests": []
}
}
}
},
"engines": {
"f1ed5b40-6a26-4eac-a2b8-9960516e4164": {
"key": "f1ed5b40-6a26-4eac-a2b8-9960516e4164",
"enabled": false,
"name": "PacBio CoA installation"
},
"pacbio-hpc": {
"key": "pacbio-hpc",
"enabled": true,
"name": "pacbio-hpc"
}
},
"test_params": {
"global_params": {
"sample_id": "HG005",
"reference_name": "GRCh38",
"default_runtime_attributes": {
"preemptible_tries": 3,
"max_retries": 3,
"zones": "",
"queue_arn": "",
"container_registry": "quay.io/pacbio"
},
"on_demand_runtime_attributes": {
"preemptible_tries": 0,
"max_retries": 0,
"zones": "",
"queue_arn": "",
"container_registry": "quay.io/pacbio"
}
},
"engine_params": {
"f1ed5b40-6a26-4eac-a2b8-9960516e4164": {
"input_file_path": "/coac74908838b5dd7/inputs/small_dataset/chr6.p23",
"resources_file_path": "/coac74908838b5dd7/inputs/wdl-ci/humanassembly",
"datasets_file_path": "/datasetpbrarediseases/dataset"
},
"pacbio-hpc": {
"input_file_path": "/pbi/collections/appslabht/cromwell_output/testdata/inputs/chr6.p23",
"resources_file_path": "/pbi/collections/appslabht/cromwell_output/testdata/wdl-ci/humanassembly",
"datasets_file_path": "/pbi/collections/appslabht/cromwell_output/testdata/datasetpbrarediseases/dataset"
}
}
}
}