diff --git a/README.md b/README.md index 445eee9..5de4588 100644 --- a/README.md +++ b/README.md @@ -24,18 +24,18 @@ Both workflows are designed to analyze human PacBio whole genome sequencing (WGS This is an actively developed workflow with multiple versioned releases, and we make use of git submodules for common tasks that are shared by multiple workflows. There are two ways to ensure you are using a supported release of the workflow and ensure that the submodules are correctly initialized: -1) Download the release zips directly from a [supported release](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/tag/v2.0.6): +1) Download the release zips directly from a [supported release](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/tag/v2.0.7): ```bash - wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.0.6/hifi-human-wgs-singleton.zip - wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.0.6/hifi-human-wgs-family.zip + wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.0.7/hifi-human-wgs-singleton.zip + wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.0.7/hifi-human-wgs-family.zip ``` 2) Clone the repository and initialize the submodules: ```bash git clone \ - --depth 1 --branch v2.0.6 \ + --depth 1 --branch v2.0.7 \ --recursive \ https://github.com/PacificBiosciences/HiFi-human-WGS-WDL.git ``` diff --git a/wdl-ci.config.json b/wdl-ci.config.json index e1d8eb5..adc4337 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -37,18 +37,141 @@ "tasks": { "slivar_small_variant": { "key": "slivar_small_variant", - "digest": "", - "tests": [] + "digest": "nz7zrdaatasxka5rziksdmc2oq4tr23z", + "tests": [ + { + "inputs": { + "vcf": "${resources_file_path}/slivar_small_variant/input/HG002-trio.GRCh38.small_variants.vcf.gz", + "vcf_index": "${resources_file_path}/slivar_small_variant/input/HG002-trio.GRCh38.small_variants.vcf.gz.tbi", + "pedigree": "${resources_file_path}/slivar_small_variant/input/HG002-trio.ped", + "phrank_lookup": "${resources_file_path}/slivar_small_variant/input/HG002-trio_phrank.tsv", + "reference": "${ref_fasta}", + "reference_index": "${ref_index}", + "gff": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/ensembl.GRCh38.101.reformatted.gff3.gz", + "lof_lookup": "${resources_file_path}/hifi-wdl-resources-v2.0.0/slivar/lof_lookup.v2.1.1.txt", + "clinvar_lookup": "${resources_file_path}/hifi-wdl-resources-v2.0.0/slivar/clinvar_gene_desc.20240624T165443.txt", + "slivar_js": "${resources_file_path}/hifi-wdl-resources-v2.0.0/slivar/slivar-functions.v0.2.8.js", + "gnotate_files": [ + "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/slivar_gnotate/gnomad.hg38.v4.1.custom.v1.zip", + "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/slivar_gnotate/CoLoRSdb.GRCh38.v1.1.0.deepvariant.glnexus.zip" + ], + "af_expr": [ + "INFO.gnomad_af <= 0.03", + "INFO.colors_af <= 0.03" + ], + "nhomalt_expr": [ + "INFO.gnomad_nhomalt <= 4", + "INFO.colors_nhomalt <= 4" + ], + "ac_expr": [ + "INFO.gnomad_ac <= 4", + "INFO.colors_ac <= 4" + ], + "info_fields": [ + "gnomad_af", + "gnomad_nhomalt", + "gnomad_ac", + "colors_af", + "colors_nhomalt", + "colors_ac" + ], + "min_gq": "5", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "filtered_vcf": { + "value": "${resources_file_path}/slivar_small_variant/output/HG002-trio.GRCh38.small_variants.norm.slivar.vcf.gz", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + }, + "compound_het_vcf": { + "value": "${resources_file_path}/slivar_small_variant/output/HG002-trio.GRCh38.small_variants.norm.slivar.compound_hets.vcf.gz", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + }, + "filtered_tsv": { + "value": "${resources_file_path}/slivar_small_variant/output/HG002-trio.GRCh38.small_variants.norm.slivar.tsv", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns" + ] + }, + "compound_het_tsv": { + "value": "${resources_file_path}/slivar_small_variant/output/HG002-trio.GRCh38.small_variants.norm.slivar.compound_hets.tsv", + "test_tasks": [ + 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"${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/ensembl.GRCh38.101.reformatted.gff3.gz", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "svpack_vcf": { + "value": "${resources_file_path}/svpack_filter_annotated/output/HG002-trio.GRCh38.structural_variants.svpack.vcf.gz", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + } + } + } + ] }, "slivar_svpack_tsv": { "key": "slivar_svpack_tsv", - "digest": "", - "tests": [] + "digest": "nyawjsg47zrbjodngljbicaww2mqsspc", + "tests": [ + { + "inputs": { + "filtered_vcf": "${resources_file_path}/slivar_svpack_tsv/input/HG002-trio.GRCh38.structural_variants.svpack.vcf.gz", + "pedigree": "${resources_file_path}/slivar_svpack_tsv/input/HG002-trio.ped", + "lof_lookup": "${resources_file_path}/hifi-wdl-resources-v2.0.0/slivar/lof_lookup.v2.1.1.txt", + "clinvar_lookup": "${resources_file_path}/hifi-wdl-resources-v2.0.0/slivar/clinvar_gene_desc.20240624T165443.txt", + "phrank_lookup": "${resources_file_path}/slivar_svpack_tsv/input/HG002-trio_phrank.tsv", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "svpack_tsv": { + "value": "${resources_file_path}/slivar_svpack_tsv/output/HG002-trio.GRCh38.structural_variants.svpack.tsv", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns" + ] + } + } + } + ] } } }, @@ -71,28 +194,388 @@ "tasks": { "bcftools_stats_roh_small_variants": { "key": "bcftools_stats_roh_small_variants", - "digest": "", - "tests": [] + "digest": "abrbvw7exjpg4zshsttwosmgoo75f722", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "vcf": "${resources_file_path}/bcftools_stats_roh_small_variants/input/from_deepvariant/HG002.GRCh38.small_variants.phased.chr6_10000000_20000000.phased.vcf.gz", + "ref_fasta": "${ref_fasta}", + "ref_name": "${ref_name}", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "stats": { + "value": 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"${resources_file_path}/bcftools_merge/input/trgt/HG004.GRCh38.trgt.sorted.phased.chr6_10000000_20000000.phased.vcf.gz" + ], + "vcf_indices": [ + "${resources_file_path}/bcftools_merge/input/trgt/HG002.GRCh38.trgt.sorted.phased.chr6_10000000_20000000.phased.vcf.gz.tbi", + "${resources_file_path}/bcftools_merge/input/trgt/HG003.GRCh38.trgt.sorted.phased.chr6_10000000_20000000.phased.vcf.gz.tbi", + "${resources_file_path}/bcftools_merge/input/trgt/HG004.GRCh38.trgt.sorted.phased.chr6_10000000_20000000.phased.vcf.gz.tbi" + ], + "out_prefix": "HG002-trio.GRCh38.trgt", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "merged_vcf": { + "value": "${resources_file_path}/bcftools_merge/output/trgt/HG002-trio.GRCh38.trgt.vcf.gz", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + } + } + } + ] }, "sv_stats": { "key": "sv_stats", - "digest": "", - "tests": [] + "digest": "35gn2cqouobao6vacrqbi67zhkh6nmyn", + "tests": [ + { + "inputs": { + "vcf": "${resources_file_path}/sv_stats/HG002.GRCh38.pbsv.phased.vcf.gz", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "stat_sv_DUP_count": { + "value": "2", + "test_tasks": [ + "compare_string" + ] + }, + "stat_sv_DEL_count": { + "value": "19", + "test_tasks": [ + "compare_string" + ] + }, + "stat_sv_INS_count": { + "value": "37", + "test_tasks": [ + "compare_string" + ] + }, + "stat_sv_INV_count": { + "value": "1", + "test_tasks": [ + "compare_string" + ] + }, + "stat_sv_BND_count": { + "value": "0", + "test_tasks": [ + "compare_string" + ] + } + } + } + ] } } }, @@ -103,8 +586,87 @@ "tasks": { "cpg_pileup": { "key": "cpg_pileup", - "digest": "", - "tests": [] + "digest": "noq7e5yf5h6s2sf7lzolbgigqec4izmg", + "tests": [ + { + "inputs": { + "haplotagged_bam": "${resources_file_path}/inputs/HG002.GRCh38.haplotagged.bam", + "haplotagged_bam_index": "${resources_file_path}/inputs/HG002.GRCh38.haplotagged.bam.bai", + "out_prefix": "HG002.GRCh38", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "combined_bed": { + "value": "${resources_file_path}/cpg_pileup/HG002.GRCh38.cpg_pileup.combined.bed.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_bed_columns", + "check_gzip" + ] + }, + "hap1_bed": { + "value": "${resources_file_path}/cpg_pileup/HG002.GRCh38.cpg_pileup.hap1.bed.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_bed_columns", + "check_gzip" + ] + }, + "hap2_bed": { + "value": "${resources_file_path}/cpg_pileup/HG002.GRCh38.cpg_pileup.hap2.bed.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_bed_columns", + "check_gzip" + ] + }, + "combined_bw": { + "value": "${resources_file_path}/cpg_pileup/HG002.GRCh38.cpg_pileup.combined.bw", + "test_tasks": [ + "compare_file_basename", + "bigwig_validator" + ] + }, + "hap1_bw": { + "value": "${resources_file_path}/cpg_pileup/HG002.GRCh38.cpg_pileup.hap1.bw", + "test_tasks": [ + "compare_file_basename", + "bigwig_validator" + ] + }, + "hap2_bw": { + "value": "${resources_file_path}/cpg_pileup/HG002.GRCh38.cpg_pileup.hap2.bw", + "test_tasks": [ + "compare_file_basename", + "bigwig_validator" + ] + }, + "stat_hap1_cpg_count": { + "value": "104635", + "test_tasks": [ + "compare_string" + ] + }, + "stat_hap2_cpg_count": { + "value": "104728", + "test_tasks": [ + "compare_string" + ] + }, + "stat_combined_cpg_count": { + "value": "106430", + "test_tasks": [ + "compare_string" + ] + } + } + } + ] } } }, @@ -115,8 +677,36 @@ "tasks": { "glnexus": { "key": "glnexus", - "digest": "", - "tests": [] + "digest": "3qe7sprlc7n62p6ozbxkva2xkkn4snlq", + "tests": [ + { + "inputs": { + "cohort_id": "HG002-trio", + "gvcfs": [ + "${resources_file_path}/inputs/HG002.GRCh38.small_variants.chr6_10000000_20000000.g.vcf.gz", + "${resources_file_path}/inputs/HG003.GRCh38.small_variants.chr6_10000000_20000000.g.vcf.gz", + "${resources_file_path}/inputs/HG004.GRCh38.small_variants.chr6_10000000_20000000.g.vcf.gz" + ], + "gvcf_indices": [ + "${resources_file_path}/inputs/HG002.GRCh38.small_variants.chr6_10000000_20000000.g.vcf.gz.tbi", + "${resources_file_path}/inputs/HG003.GRCh38.small_variants.chr6_10000000_20000000.g.vcf.gz.tbi", + "${resources_file_path}/inputs/HG004.GRCh38.small_variants.chr6_10000000_20000000.g.vcf.gz.tbi" + ], + "ref_name": "${ref_name}", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "vcf": { + "value": "${resources_file_path}/glnexus/HG002-trio.GRCh38.small_variants.vcf.gz", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + } + } + } + ] } } }, @@ -127,8 +717,83 @@ "tasks": { "hificnv": { "key": "hificnv", - "digest": "", - "tests": [] + "digest": "kswxkn6zzlkuucuumxqbiaq5cx2sdiki", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "sex": "MALE", + "aligned_bam": "${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.bam", + "aligned_bam_index": "${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.bam.bai", + "vcf": "${resources_file_path}/inputs/HG002.GRCh38.small_variants.vcf.gz", + "vcf_index": "${resources_file_path}/inputs/HG002.GRCh38.small_variants.vcf.gz", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "ref_name": "${ref_name}", + "exclude_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz", + "exclude_bed_index": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz.tbi", + "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", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "cnv_vcf": { + "value": "${resources_file_path}/hificnv/HG002.GRCh38.hificnv.vcf.gz", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + }, + "copynum_bedgraph": { + "value": "${resources_file_path}/hificnv/HG002.GRCh38.hificnv.copynum.bedgraph", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_bed_columns" + ] + }, + "depth_bw": { + "value": "${resources_file_path}/hificnv/HG002.GRCh38.hificnv.depth.bw", + "test_tasks": [ + "compare_file_basename", + "bigwig_validator" + ] + }, + "maf_bw": { + "value": "${resources_file_path}/hificnv/HG002.GRCh38.hificnv.maf.bw", + "test_tasks": [ + "compare_file_basename", + "bigwig_validator" + ] + }, + "stat_DUP_count": { + "value": "0", + "test_tasks": [ + "compare_string" + ] + }, + "stat_DUP_sum": { + "value": "0", + "test_tasks": [ + "compare_string" + ] + }, + "stat_DEL_count": { + "value": "89", + "test_tasks": [ + "compare_string" + ] + }, + "stat_DEL_sum": { + "value": "2885534000", + "test_tasks": [ + "compare_string" + ] + } + } + } + ] } } }, @@ -139,8 +804,126 @@ "tasks": { "hiphase": { "key": "hiphase", - "digest": "", - "tests": [] + "digest": "evdi2klxze7sag3fs4p6g4h4ffqmiqzy", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "vcfs": [ + "${resources_file_path}/hiphase/input/HG002/HG002.GRCh38.small_variants.vcf.gz", + "${resources_file_path}/hiphase/input/HG002/HG002.GRCh38.pbsv.vcf.gz", + "${resources_file_path}/hiphase/input/HG002/HG002.GRCh38.trgt.sorted.vcf.gz" + ], + "vcf_indices": [ + "${resources_file_path}/hiphase/input/HG002/HG002.GRCh38.small_variants.vcf.gz.tbi", + "${resources_file_path}/hiphase/input/HG002/HG002.GRCh38.pbsv.vcf.gz.tbi", + "${resources_file_path}/hiphase/input/HG002/HG002.GRCh38.trgt.sorted.vcf.gz.tbi" + ], + "phased_vcf_names": [ + "HG002.GRCh38.small_variants.phased.vcf.gz", + "HG002.GRCh38.pbsv.phased.vcf.gz", + "HG002.GRCh38.trgt.sorted.phased.vcf.gz" + ], + "phased_vcf_index_names": [ + "HG002.GRCh38.small_variants.phased.vcf.gz.tbi", + "HG002.GRCh38.pbsv.phased.vcf.gz.tbi", + "HG002.GRCh38.trgt.sorted.phased.vcf.gz.tbi" + ], + "aligned_bam": "${resources_file_path}/hiphase/input/HG002/HG002.GRCh38.chr6_10000000_20000000.bam", + "aligned_bam_index": "${resources_file_path}/hiphase/input/HG002/HG002.GRCh38.chr6_10000000_20000000.bam.bai", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "ref_name": "${ref_name}", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "phased_vcfs": { + "value": [ + "${resources_file_path}/hiphase/output/HG002/HG002.GRCh38.small_variants.phased.vcf.gz", + "${resources_file_path}/hiphase/output/HG002/HG002.GRCh38.pbsv.phased.vcf.gz", + "${resources_file_path}/hiphase/output/HG002/HG002.GRCh38.trgt.sorted.phased.vcf.gz" + ], + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + }, + "haplotagged_bam": { + "value": "${resources_file_path}/hiphase/output/HG002/HG002.GRCh38.haplotagged.bam", + "test_tasks": [ + "compare_file_basename", + "samtools_quickcheck" + ] + }, + "phase_stats": { + "value": "${resources_file_path}/hiphase/output/HG002/HG002.GRCh38.hiphase.stats.tsv", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns" + ] + }, + "phase_blocks": { + "value": "${resources_file_path}/hiphase/output/HG002/HG002.GRCh38.hiphase.blocks.tsv", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns" + ] + }, + "phase_haplotags": { + "value": "${resources_file_path}/hiphase/output/HG002/HG002.GRCh38.hiphase.haplotags.tsv.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "check_gzip" + ] + }, + "stat_phased_basepairs": { + "value": "8972304", + "test_tasks": [ + "compare_string" + ] + }, + "stat_phase_block_ng50": { + "value": "0", + "test_tasks": [ + "compare_string" + ] + }, + "stat_mapped_read_count": { + "value": "27398", + "test_tasks": [ + "compare_string" + ] + }, + "stat_mapped_percent": { + "value": "100", + "test_tasks": [ + "compare_string" + ] + }, + "mapq_distribution_plot": { + "value": "${resources_file_path}/hiphase/output/HG002/HG002.GRCh38.mapq_distribution.png", + "test_tasks": [ + "calculate_md5sum", + "compare_file_basename", + "png_validator" + ] + }, + "mg_distribution_plot": { + "value": "${resources_file_path}/hiphase/output/HG002/HG002.GRCh38.mg_distribution.png", + "test_tasks": [ + "calculate_md5sum", + "compare_file_basename", + "png_validator" + ] + } + } + } + ] } } }, @@ -151,8 +934,142 @@ "tasks": { "merge_bam_stats": { "key": "merge_bam_stats", - "digest": "", - "tests": [] + "digest": "k2zoxoqmson4rr7meogbb675w3bnj2gt", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "bam_stats": [ + "${resources_file_path}/pbmm2_align_wgs/sequelii_kinetics_10k/HG00133.sequelii_kinetics_10k.hifi_reads.read_length_and_quality.tsv.gz" + ], + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "read_length_and_quality": { + "value": "${resources_file_path}/merge_bam_stats/one_input/HG002.read_length_and_quality.tsv.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "check_gzip" + ] + }, + "read_length_plot": { + "value": "${resources_file_path}/merge_bam_stats/one_input/HG002.read_length_histogram.png", + "test_tasks": [ + "calculate_md5sum", + "compare_file_basename", + "png_validator" + ] + }, + "read_quality_plot": { + "value": "${resources_file_path}/merge_bam_stats/one_input/HG002.read_quality_histogram.png", + "test_tasks": [ + "calculate_md5sum", + "compare_file_basename", + "png_validator" + ] + }, + "stat_num_reads": { + "value": "10000", + "test_tasks": [ + "compare_string" + ] + }, + "stat_read_length_mean": { + "value": "23508.73", + "test_tasks": [ + "compare_string" + ] + }, + "stat_read_length_median": { + "value": "22855.5", + "test_tasks": [ + "compare_string" + ] + }, + "stat_read_quality_mean": { + "value": "26.97", + "test_tasks": [ + "compare_string" + ] + }, + "stat_read_quality_median": { + "value": "27.0", + "test_tasks": [ + "compare_string" + ] + } + } + }, + { + "inputs": { + "sample_id": "HG002", + "bam_stats": [ + "${resources_file_path}/pbmm2_align_wgs/sequelii_kinetics_10k/HG00133.sequelii_kinetics_10k.hifi_reads.read_length_and_quality.tsv.gz", + "${resources_file_path}/pbmm2_align_wgs/vega_10k/HG002.vega_10k.hifi_reads.read_length_and_quality.tsv.gz" + ], + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "read_length_and_quality": { + "value": "${resources_file_path}/merge_bam_stats/two_inputs/HG002.read_length_and_quality.tsv.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "check_gzip" + ] + }, + "read_length_plot": { + "value": "${resources_file_path}/merge_bam_stats/two_inputs/HG002.read_length_histogram.png", + "test_tasks": [ + "calculate_md5sum", + "compare_file_basename", + "png_validator" + ] + }, + "read_quality_plot": { + "value": "${resources_file_path}/merge_bam_stats/two_inputs/HG002.read_quality_histogram.png", + "test_tasks": [ + "calculate_md5sum", + "compare_file_basename", + "png_validator" + ] + }, + "stat_num_reads": { + "value": "20000", + "test_tasks": [ + "compare_string" + ] + }, + "stat_read_length_mean": { + "value": "22673.07", + "test_tasks": [ + "compare_string" + ] + }, + "stat_read_length_median": { + "value": "22281.5", + "test_tasks": [ + "compare_string" + ] + }, + "stat_read_quality_mean": { + "value": "29.32", + "test_tasks": [ + "compare_string" + ] + }, + "stat_read_quality_median": { + "value": "29.0", + "test_tasks": [ + "compare_string" + ] + } + } + } + ] } } }, @@ -163,8 +1080,108 @@ "tasks": { "mosdepth": { "key": "mosdepth", - "digest": "", - "tests": [] + "digest": "57rmcwxx2lmhgupdu4unxkldevrr3n3u", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "ref_name": "${ref_name}", + "aligned_bam": "${resources_file_path}/pbmm2_align_wgs/vega_10k/HG002.vega_10k.hifi_reads.GRCh38.aligned.bam", + "aligned_bam_index": "${resources_file_path}/pbmm2_align_wgs/vega_10k/HG002.vega_10k.hifi_reads.GRCh38.aligned.bam.bai", + "infer_sex": true, + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "summary": { + "value": "${resources_file_path}/mosdepth/infer_sex/HG002.GRCh38.mosdepth.summary.txt", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + }, + "region_bed": { + "value": "${resources_file_path}/mosdepth/infer_sex/HG002.GRCh38.regions.bed.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_bed_columns", + "check_gzip" + ] + }, + "depth_distribution_plot": { + "value": "${resources_file_path}/mosdepth/infer_sex/HG002.GRCh38.depth_distribution.png", + "test_tasks": [ + "calculate_md5sum", + "compare_file_basename", + "png_validator" + ] + }, + "stat_mean_depth": { + "value": "0.07", + "test_tasks": [ + "compare_string" + ] + }, + "inferred_sex": { + "value": "MALE", + "test_tasks": [ + "compare_string" + ] + } + } + }, + { + "inputs": { + "sample_id": "HG002", + "ref_name": "${ref_name}", + "aligned_bam": "${resources_file_path}/pbmm2_align_wgs/vega_10k/HG002.vega_10k.hifi_reads.GRCh38.aligned.bam", + "aligned_bam_index": "${resources_file_path}/pbmm2_align_wgs/vega_10k/HG002.vega_10k.hifi_reads.GRCh38.aligned.bam.bai", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "summary": { + "value": "${resources_file_path}/mosdepth/no_infer_sex/HG002.GRCh38.mosdepth.summary.txt", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + }, + "region_bed": { + "value": "${resources_file_path}/mosdepth/no_infer_sex/HG002.GRCh38.regions.bed.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_bed_columns", + "check_gzip" + ] + }, + "depth_distribution_plot": { + "value": "${resources_file_path}/mosdepth/no_infer_sex/HG002.GRCh38.depth_distribution.png", + "test_tasks": [ + "calculate_md5sum", + "compare_file_basename", + "png_validator" + ] + }, + "stat_mean_depth": { + "value": "0.07", + "test_tasks": [ + "compare_string" + ] + }, + "inferred_sex": { + "value": "", + "test_tasks": [ + "compare_string" + ] + } + } + } + ] } } }, @@ -175,8 +1192,42 @@ "tasks": { "paraphase": { "key": "paraphase", - "digest": "", - "tests": [] + "digest": "bxbomtn5ohxnrus7l4rxkbda5xpgrgag", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "aligned_bam": "${resources_file_path}/inputs/HG002.GRCh38.paraphase_regions.bam", + "aligned_bam_index": "${resources_file_path}/inputs/HG002.GRCh38.paraphase_regions.bam.bai", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "out_json": { + "value": "${resources_file_path}/paraphase/HG002.paraphase.json", + "test_tasks": [ + "compare_file_basename", + "check_json" + ] + }, + "bam": { + "value": "${resources_file_path}/paraphase/HG002.paraphase.bam", + "test_tasks": [ + "compare_file_basename", + "samtools_quickcheck" + ] + }, + "vcfs_tar": { + "value": "${resources_file_path}/paraphase/HG002.paraphase_vcfs.tar.gz", + "test_tasks": [ + "compare_file_basename", + "check_gzip" + ] + } + } + } + ] } } }, @@ -187,8 +1238,122 @@ "tasks": { "pbmm2_align_wgs": { "key": "pbmm2_align_wgs", - "digest": "", - "tests": [] + "digest": "r2mrlrcc34hmpeetxabc7ujwfb2zzykq", + "tests": [ + { + "inputs": { + "sample_id": "HG00733", + "bam": "${resources_file_path}/inputs/sequelii_aligned_10k.hifi_reads.bam", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "ref_name": "${ref_name}", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "aligned_bam": { + "value": "${resources_file_path}/pbmm2_align_wgs/sequelii_aligned_10k/HG00733.sequelii_aligned_10k.hifi_reads.GRCh38.aligned.bam", + "test_tasks": [ + "compare_file_basename", + "samtools_quickcheck" + ] + }, + "bam_stats": { + "value": "${resources_file_path}/pbmm2_align_wgs/sequelii_aligned_10k/HG00733.sequelii_aligned_10k.hifi_reads.read_length_and_quality.tsv.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "check_gzip" + ] + } + } + }, + { + "inputs": { + "sample_id": "HG00133", + "bam": "${resources_file_path}/inputs/sequelii_kinetics_10k.hifi_reads.bam", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "ref_name": "${ref_name}", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "aligned_bam": { + "value": "${resources_file_path}/pbmm2_align_wgs/sequelii_kinetics_10k/HG00133.sequelii_kinetics_10k.hifi_reads.GRCh38.aligned.bam", + "test_tasks": [ + "compare_file_basename", + "samtools_quickcheck" + ] + }, + "bam_stats": { + "value": "${resources_file_path}/pbmm2_align_wgs/sequelii_kinetics_10k/HG00133.sequelii_kinetics_10k.hifi_reads.read_length_and_quality.tsv.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "check_gzip" + ] + } + } + }, + { + "inputs": { + "sample_id": "HG00133", + "bam": "${resources_file_path}/inputs/sequelii_kinetics_10k.hifi_reads.bam", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "ref_name": "${ref_name}", + "strip_kinetics": false, + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "aligned_bam": { + "value": "${resources_file_path}/pbmm2_align_wgs/sequelii_kinetics_10k_strip_kinetics_false/HG00133.sequelii_kinetics_10k.hifi_reads.GRCh38.aligned.bam", + "test_tasks": [ + "compare_file_basename", + "samtools_quickcheck" + ] + }, + "bam_stats": { + "value": "${resources_file_path}/pbmm2_align_wgs/sequelii_kinetics_10k_strip_kinetics_false/HG00133.sequelii_kinetics_10k.hifi_reads.read_length_and_quality.tsv.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "check_gzip" + ] + } + } + }, + { + "inputs": { + "sample_id": "HG002", + "bam": "${resources_file_path}/inputs/vega_10k.hifi_reads.bam", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "ref_name": "${ref_name}", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "aligned_bam": { + "value": "${resources_file_path}/pbmm2_align_wgs/vega_10k/HG002.vega_10k.hifi_reads.GRCh38.aligned.bam", + "test_tasks": [ + "compare_file_basename", + "samtools_quickcheck" + ] + }, + "bam_stats": { + "value": "${resources_file_path}/pbmm2_align_wgs/vega_10k/HG002.vega_10k.hifi_reads.read_length_and_quality.tsv.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "check_gzip" + ] + } + } + } + ] } } }, @@ -199,8 +1364,38 @@ "tasks": { "pbstarphase_diplotype": { "key": "pbstarphase_diplotype", - "digest": "", - "tests": [] + "digest": "q4p6pxx4sxdrghgrb2eirppmxayc5tuf", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "phased_vcf": "${resources_file_path}/pbstarphase_diplotype/input/HG002.GRCh38.subset.small_variants.vcf.gz", + "phased_vcf_index": "${resources_file_path}/pbstarphase_diplotype/input/HG002.GRCh38.subset.small_variants.vcf.gz.tbi", + "aligned_bam": "${resources_file_path}/pbstarphase_diplotype/input/HG002.GRCh38.subset.bam", + "aligned_bam_index": "${resources_file_path}/pbstarphase_diplotype/input/HG002.GRCh38.subset.bam.bai", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "out_json": { + "value": "${resources_file_path}/pbstarphase_diplotype/output/HG002.pbstarphase.json", + "test_tasks": [ + "compare_file_basename", + "check_json" + ] + }, + "pharmcat_tsv": { + "value": "${resources_file_path}/pbstarphase_diplotype/output/HG002.pharmcat.tsv", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns" + ] + } + } + } + ] } } }, @@ -211,13 +1406,110 @@ "tasks": { "pbsv_discover": { "key": "pbsv_discover", - "digest": "", - "tests": [] + "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": "${resources_file_path}/pbsv_discover/HG002.GRCh38.chr6_10000000_20000000.svsig.gz", + "test_tasks": [ + "compare_file_basename", + "check_gzip", + "check_empty_lines" + ] + } + } + } + ] }, "pbsv_call": { "key": "pbsv_call", - "digest": "", - "tests": [] + "digest": "2rhytrhz52jofq7lv42akixzl55wa3lk", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "svsigs": [ + "${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": "${resources_file_path}/pbsv_call/trio/HG002-trio.GRCh38.5.pbsv.vcf.gz", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + } + } + } + ] } } }, @@ -228,8 +1520,28 @@ "tasks": { "samtools_merge": { "key": "samtools_merge", - "digest": "", - "tests": [] + "digest": "lmc2sfyir2g2cile2vwmaatp46vzddbs", + "tests": [ + { + "inputs": { + "bams": [ + "${resources_file_path}/samtools_merge/input/HG00133.sequelii_kinetics_10k.hifi_reads.GRCh38.aligned.bam", + "${resources_file_path}/samtools_merge/input/HG002.vega_10k.hifi_reads.GRCh38.aligned.bam" + ], + "out_prefix": "HG002HG00133.GRCh38", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "merged_bam": { + "value": "${resources_file_path}/samtools_merge/output/two_inputs/HG002HG00133.GRCh38.bam", + "test_tasks": [ + "compare_file_basename", + "samtools_quickcheck" + ] + } + } + } + ] }, "samtools_fasta": { "key": "samtools_fasta", @@ -250,18 +1562,151 @@ "tasks": { "trgt": { "key": "trgt", - "digest": "", - "tests": [] + "digest": "rpcfzfr5reqxv7jbtfncu6etivzxvgs2", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "aligned_bam": "${resources_file_path}/trgt/input/HG002.vega_10k.hifi_reads.GRCh38.aligned.bam", + "aligned_bam_index": "${resources_file_path}/trgt/input/HG002.vega_10k.hifi_reads.GRCh38.aligned.bam.bai", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "trgt_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed", + "out_prefix": "HG002.GRCh38", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "bam": { + "value": "${resources_file_path}/trgt/output/no_sex/HG002.GRCh38.trgt.spanning.sorted.bam", + "test_tasks": [ + "compare_file_basename", + "samtools_quickcheck" + ] + }, + "vcf": { + "value": "${resources_file_path}/trgt/output/no_sex/HG002.GRCh38.trgt.sorted.vcf.gz", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + }, + "stat_genotyped_count": { + "value": "9163", + "test_tasks": [ + "compare_string" + ] + }, + "stat_uncalled_count": { + "value": "162039", + "test_tasks": [ + "compare_string" + ] + } + } + }, + { + "inputs": { + "sample_id": "HG002", + "sex": "MALE", + "aligned_bam": "${resources_file_path}/trgt/input/HG002.vega_10k.hifi_reads.GRCh38.aligned.bam", + "aligned_bam_index": "${resources_file_path}/trgt/input/HG002.vega_10k.hifi_reads.GRCh38.aligned.bam.bai", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "trgt_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed", + "out_prefix": "HG002.GRCh38", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "bam": { + "value": "${resources_file_path}/trgt/output/with_sex/HG002.GRCh38.trgt.spanning.sorted.bam", + "test_tasks": [ + "compare_file_basename", + "samtools_quickcheck" + ] + }, + "vcf": { + "value": "${resources_file_path}/trgt/output/with_sex/HG002.GRCh38.trgt.sorted.vcf.gz", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + }, + "stat_genotyped_count": { + "value": "9163", + "test_tasks": [ + "compare_string" + ] + }, + "stat_uncalled_count": { + "value": "162039", + "test_tasks": [ + "compare_string" + ] + } + } + } + ] }, "trgt_merge": { "key": "trgt_merge", - "digest": "", - "tests": [] + "digest": "cmdcqkqrcfpn2eoczxfwhs6zqhalzdtt", + "tests": [ + { + "inputs": { + "vcfs": [ + "${resources_file_path}/trgt_merge/input/HG002-trio/HG002.GRCh38.trgt.sorted.phased.chr6_10000000_20000000.vcf.gz", + "${resources_file_path}/trgt_merge/input/HG002-trio/HG003.GRCh38.trgt.sorted.phased.chr6_10000000_20000000.vcf.gz", + "${resources_file_path}/trgt_merge/input/HG002-trio/HG004.GRCh38.trgt.sorted.phased.chr6_10000000_20000000.vcf.gz" + ], + "vcf_indices": [ + "${resources_file_path}/trgt_merge/input/HG002-trio/HG002.GRCh38.trgt.sorted.phased.chr6_10000000_20000000.vcf.gz.tbi", + "${resources_file_path}/trgt_merge/input/HG002-trio/HG003.GRCh38.trgt.sorted.phased.chr6_10000000_20000000.vcf.gz.tbi", + "${resources_file_path}/trgt_merge/input/HG002-trio/HG004.GRCh38.trgt.sorted.phased.chr6_10000000_20000000.vcf.gz.tbi" + ], + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "out_prefix": "HG002-trio.GRCh38.trgt", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "merged_vcf": { + "value": "${resources_file_path}/trgt_merge/output/HG002-trio/HG002-trio.GRCh38.trgt.vcf.gz", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + } + } + } + ] }, "coverage_dropouts": { "key": "coverage_dropouts", - "digest": "", - "tests": [] + "digest": "k6fkzuz3gk4yqc555nov2io3qbeqe25h", + "tests": [ + { + "inputs": { + "aligned_bam": "${resources_file_path}/trgt/input/HG002.vega_10k.hifi_reads.GRCh38.aligned.bam", + "aligned_bam_index": "${resources_file_path}/trgt/input/HG002.vega_10k.hifi_reads.GRCh38.aligned.bam.bai", + "trgt_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed", + "out_prefix": "HG002.GRCh38", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "dropouts": { + "value": "${resources_file_path}/coverage_dropouts/HG002.GRCh38.trgt.dropouts.txt", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns" + ] + } + } + } + ] } } }, @@ -272,13 +1717,61 @@ "tasks": { "split_string": { "key": "split_string", - "digest": "", - "tests": [] + "digest": "q7byrkraoxoid54g6rnw32zejprmobk6", + "tests": [ + { + "inputs": { + "concatenated_string": "hello,world", + "delimiter": ",", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "array": { + "value": [ + "hello", + "world" + ], + "test_tasks": [ + "compare_string" + ] + } + } + } + ] }, "consolidate_stats": { "key": "consolidate_stats", - "digest": "", - "tests": [] + "digest": "3w2ttlxevhy2vkao2q2tj7c6n5qilxni", + "tests": [ + { + "inputs": { + "id": "String", + "stats": { + "letters": [ + "a", + "b", + "c" + ], + "numbers": [ + "1", + "2", + "3" + ] + }, + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "output_tsv": { + "value": "${resources_file_path}/consolidate_stats/String.stats.txt", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns" + ] + } + } + } + ] } } }, @@ -289,8 +1782,275 @@ "tasks": { "write_ped_phrank": { "key": "write_ped_phrank", - "digest": "", - "tests": [] + "digest": "d3b7uvydynagkxs2w546ozi7q6oa7cim", + "tests": [ + { + "inputs": { + "id": "HG002", + "sex": "MALE", + "phenotypes": "HP:0000001", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "pedigree": { + "value": "${resources_file_path}/write_ped_phrank/output/singleton/HG002.ped", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + }, + "phrank_lookup": { + "value": "${resources_file_path}/write_ped_phrank/output/singleton/HG002_phrank.tsv", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + } + } + }, + { + "inputs": { + "id": "HG002", + "phenotypes": "HP:0000001", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "pedigree": { + "value": "${resources_file_path}/write_ped_phrank/output/singleton_no_sex/HG002.ped", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + }, + "phrank_lookup": { + "value": "${resources_file_path}/write_ped_phrank/output/singleton_no_sex/HG002_phrank.tsv", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + } + } + }, + { + "inputs": { + "id": "HG002-trio", + "family": { + "family_id": "HG002-trio", + "samples": [ + { + "sample_id": "HG002", + "sex": "MALE", + "affected": true, + "father_id": "HG003", + "mother_id": "HG004", + "hifi_reads": [ + "${resources_file_path}/write_ped_phrank/input/dummy.bam" + ] + }, + { + "sample_id": "HG003", + "sex": "MALE", + "affected": false, + "hifi_reads": [ + "${resources_file_path}/write_ped_phrank/input/dummy.bam" + ] + }, + { + "sample_id": "HG004", + "sex": "FEMALE", + "affected": false, + "hifi_reads": [ + "${resources_file_path}/write_ped_phrank/input/dummy.bam" + ] + } + ] + }, + "phenotypes": "HP:0000001", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "pedigree": { + "value": "${resources_file_path}/write_ped_phrank/output/trio/HG002-trio.ped", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + }, + "phrank_lookup": { + "value": "${resources_file_path}/write_ped_phrank/output/trio/HG002-trio_phrank.tsv", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + } + } + }, + { + "inputs": { + "id": "HG002-trio", + "family": { + "family_id": "HG002-trio", + "samples": [ + { + "sample_id": "HG002", + "sex": "MALE", + "affected": true, + "mother_id": "HG004", + "hifi_reads": [ + "${resources_file_path}/write_ped_phrank/input/dummy.bam" + ] + }, + { + "sample_id": "HG004", + "sex": "FEMALE", + "affected": false, + "hifi_reads": [ + "${resources_file_path}/write_ped_phrank/input/dummy.bam" + ] + } + ] + }, + "phenotypes": "HP:0000001", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "pedigree": { + "value": "${resources_file_path}/write_ped_phrank/output/trio_no_father/HG002-trio.ped", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + }, + "phrank_lookup": { + "value": "${resources_file_path}/write_ped_phrank/output/trio_no_father/HG002-trio_phrank.tsv", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + } + } + }, + { + "inputs": { + "id": "HG002-trio", + "family": { + "family_id": "HG002-trio", + "samples": [ + { + "sample_id": "HG002", + "sex": "MALE", + "affected": true, + "father_id": "HG003", + "hifi_reads": [ + "${resources_file_path}/write_ped_phrank/input/dummy.bam" + ] + }, + { + "sample_id": "HG003", + "sex": "MALE", + "affected": false, + "hifi_reads": [ + "${resources_file_path}/write_ped_phrank/input/dummy.bam" + ] + } + ] + }, + "phenotypes": "HP:0000001", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "pedigree": { + "value": "${resources_file_path}/write_ped_phrank/output/trio_no_mother/HG002-trio.ped", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + }, + "phrank_lookup": { + "value": "${resources_file_path}/write_ped_phrank/output/trio_no_mother/HG002-trio_phrank.tsv", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + } + } + }, + { + "inputs": { + "id": "HG002-trio", + "family": { + "family_id": "HG002-trio", + "samples": [ + { + "sample_id": "HG002", + "affected": true, + "father_id": "HG003", + "mother_id": "HG004", + "hifi_reads": [ + "${resources_file_path}/write_ped_phrank/input/dummy.bam" + ] + }, + { + "sample_id": "HG003", + "affected": false, + "hifi_reads": [ + "${resources_file_path}/write_ped_phrank/input/dummy.bam" + ] + }, + { + "sample_id": "HG004", + "affected": false, + "hifi_reads": [ + "${resources_file_path}/write_ped_phrank/input/dummy.bam" + ] + } + ] + }, + "phenotypes": "HP:0000001", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "pedigree": { + "value": "${resources_file_path}/write_ped_phrank/output/trio_no_sex/HG002-trio.ped", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + }, + "phrank_lookup": { + "value": "${resources_file_path}/write_ped_phrank/output/trio_no_sex/HG002-trio_phrank.tsv", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "calculate_md5sum" + ] + } + } + } + ] } } }, @@ -307,23 +2067,157 @@ "tasks": { "deepvariant_make_examples": { "key": "deepvariant_make_examples", - "digest": "", - "tests": [] + "digest": "54kvpa3bz3cciywbjcwtjyb5k4ifpzhc", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "aligned_bams": [ + "${resources_file_path}/deepvariant_make_examples/input/HG002.GRCh38.chr6_10000000_20000000.bam" + ], + "aligned_bam_indices": [ + "${resources_file_path}/deepvariant_make_examples/input/HG002.GRCh38.chr6_10000000_20000000.bam.bai" + ], + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "task_start_index": 0, + "tasks_per_shard": 8, + "total_deepvariant_tasks": 64, + "docker_image": "google/deepvariant:1.6.1", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "example_tfrecord_tar": { + "value": "${resources_file_path}/deepvariant_make_examples/output/shard_0/HG002.0.example_tfrecords.tar.gz", + "test_tasks": [ + "compare_file_basename", + "check_gzip" + ] + }, + "nonvariant_site_tfrecord_tar": { + "value": "${resources_file_path}/deepvariant_make_examples/output/shard_0/HG002.0.nonvariant_site_tfrecords.tar.gz", + "test_tasks": [ + "compare_file_basename", + "check_gzip" + ] + } + } + } + ] }, "deepvariant_call_variants_cpu": { "key": "deepvariant_call_variants_cpu", - "digest": "", - "tests": [] + "digest": "vapflxnbarkmdemttze7e6f4svrtkpmw", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "ref_name": "${ref_name}", + "example_tfrecord_tars": [ + "${resources_file_path}/deepvariant_call_variants_cpu/input/HG002.0.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_cpu/input/HG002.8.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_cpu/input/HG002.16.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_cpu/input/HG002.24.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_cpu/input/HG002.32.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_cpu/input/HG002.40.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_cpu/input/HG002.48.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_cpu/input/HG002.56.example_tfrecords.tar.gz" + ], + "total_deepvariant_tasks": 64, + "docker_image": "google/deepvariant:1.6.1", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "tfrecords_tar": { + "value": "${resources_file_path}/deepvariant_call_variants_cpu/output/HG002/HG002.GRCh38.call_variants_output.tar.gz", + "test_tasks": [ + "compare_file_basename", + "check_gzip" + ] + } + } + } + ] }, "deepvariant_call_variants_gpu": { "key": "deepvariant_call_variants_gpu", - "digest": "", - "tests": [] + "digest": "4tcavedqaa6xpqet6ip4f5jxvrucjdcg", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "ref_name": "${ref_name}", + "example_tfrecord_tars": [ + "${resources_file_path}/deepvariant_call_variants_gpu/input/HG002.0.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_gpu/input/HG002.8.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_gpu/input/HG002.16.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_gpu/input/HG002.24.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_gpu/input/HG002.32.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_gpu/input/HG002.40.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_gpu/input/HG002.48.example_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_call_variants_gpu/input/HG002.56.example_tfrecords.tar.gz" + ], + "total_deepvariant_tasks": 64, + "docker_image": "google/deepvariant:1.6.1-gpu", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "tfrecords_tar": { + "value": "${resources_file_path}/deepvariant_call_variants_gpu/output/HG002/HG002.GRCh38.call_variants_output.tar.gz", + "test_tasks": [ + "compare_file_basename", + "check_gzip" + ] + } + } + } + ] }, "deepvariant_postprocess_variants": { "key": "deepvariant_postprocess_variants", - "digest": "", - "tests": [] + "digest": "xrdc7ay2sjrniggltopieawihwkunoil", + "tests": [ + { + "inputs": { + "sample_id": "HG002", + "tfrecords_tar": "${resources_file_path}/deepvariant_postprocess_variants/input/HG002.GRCh38.call_variants_output.tar.gz", + "nonvariant_site_tfrecord_tars": [ + "${resources_file_path}/deepvariant_postprocess_variants/input/HG002.0.nonvariant_site_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_postprocess_variants/input/HG002.8.nonvariant_site_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_postprocess_variants/input/HG002.16.nonvariant_site_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_postprocess_variants/input/HG002.24.nonvariant_site_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_postprocess_variants/input/HG002.32.nonvariant_site_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_postprocess_variants/input/HG002.40.nonvariant_site_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_postprocess_variants/input/HG002.48.nonvariant_site_tfrecords.tar.gz", + "${resources_file_path}/deepvariant_postprocess_variants/input/HG002.56.nonvariant_site_tfrecords.tar.gz" + ], + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "ref_name": "${ref_name}", + "total_deepvariant_tasks": 64, + "docker_image": "google/deepvariant:1.6.1", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "vcf": { + "value": "${resources_file_path}/deepvariant_postprocess_variants/output/HG002/HG002.GRCh38.small_variants.vcf.gz", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + }, + "gvcf": { + "value": "${resources_file_path}/deepvariant_postprocess_variants/output/HG002/HG002.GRCh38.small_variants.g.vcf.gz", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator", + "check_gzip" + ] + } + } + } + ] } } }, @@ -346,25 +2240,147 @@ "tasks": { "pharmcat_preprocess": { "key": "pharmcat_preprocess", - "digest": "", - "tests": [] + "digest": "2cfpsi2cznnpivx2ehkthn22rv7hkvdr", + "tests": [ + { + "inputs": { + "vcf": "${resources_file_path}/pharmcat_preprocess/input/HG002.GRCh38.subset.small_variants.vcf.gz", + "vcf_index": "${resources_file_path}/pharmcat_preprocess/input/HG002.GRCh38.subset.small_variants.vcf.gz.tbi", + "ref_fasta": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.fasta", + "ref_index": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai", + "pharmcat_positions": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/pharmcat/pharmcat_positions_2.15.4.vcf.bgz", + "pharmcat_positions_index": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/pharmcat/pharmcat_positions_2.15.4.vcf.bgz.csi", + "pharmcat_docker": "pgkb/pharmcat:2.15.4", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "missing_pgx_vcf": { + "value": "${resources_file_path}/pharmcat_preprocess/output/HG002.GRCh38.subset.small_variants.missing_pgx_var.vcf", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator" + ] + }, + "preprocessed_vcf": { + "value": "${resources_file_path}/pharmcat_preprocess/output/HG002.GRCh38.subset.small_variants.preprocessed.vcf.bgz", + "test_tasks": [ + "compare_file_basename", + "check_gzip" + ] + } + } + } + ] }, "filter_preprocessed_vcf": { "key": "filter_preprocessed_vcf", - "digest": "", - "tests": [] + "digest": "63mmofid6b46ugrq6hhmlpdc6htd767o", + "tests": [ + { + "inputs": { + "preprocessed_vcf": "${resources_file_path}/filter_preprocessed_vcf/input/HG002.GRCh38.subset.small_variants.preprocessed.vcf.bgz", + "haplotagged_bam": "${resources_file_path}/filter_preprocessed_vcf/input/HG002.GRCh38.subset.bam", + "haplotagged_bam_index": "${resources_file_path}/filter_preprocessed_vcf/input/HG002.GRCh38.subset.bam.bai", + "ref_index": "${ref_index}", + "min_coverage": 10, + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "filtered_vcf": { + "value": "${resources_file_path}/filter_preprocessed_vcf/output/HG002.GRCh38.subset.small_variants.preprocessed.filtered.vcf", + "test_tasks": [ + "compare_file_basename", + "vcftools_validator" + ] + } + } + } + ] }, "run_pharmcat": { "key": "run_pharmcat", - "digest": "", - "tests": [] + "digest": "bpvbkvx6hsvzy7a3mymzjrwqvgxdrmj7", + "tests": [ + { + "inputs": { + "preprocessed_filtered_vcf": "${resources_file_path}/run_pharmcat/input/HG002.GRCh38.subset.small_variants.preprocessed.filtered.vcf", + "input_tsvs": [ + "${resources_file_path}/run_pharmcat/input/HG002.pharmcat.tsv" + ], + "pharmcat_docker": "pgkb/pharmcat:2.15.4", + "out_prefix": "HG002.pharmcat", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "pharmcat_match_json": { + "value": "${resources_file_path}/run_pharmcat/output/HG002.pharmcat.match.json", + "test_tasks": [ + "compare_file_basename", + "check_json" + ] + }, + "pharmcat_phenotype_json": { + "value": "${resources_file_path}/run_pharmcat/output/HG002.pharmcat.phenotype.json", + "test_tasks": [ + "compare_file_basename", + "check_json" + ] + }, + "pharmcat_report_html": { + "value": "${resources_file_path}/run_pharmcat/output/HG002.pharmcat.report.html", + "test_tasks": [ + "compare_file_basename", + "check_html" + ] + }, + "pharmcat_report_json": { + "value": "${resources_file_path}/run_pharmcat/output/HG002.pharmcat.report.json", + "test_tasks": [ + "compare_file_basename", + "check_json" + ] + } + } + } + ] } } } }, - "engines": {}, + "engines": { + "pacbio-hpc": { + "key": "pacbio-hpc", + "enabled": true, + "name": "pacbio-hpc" + } + }, "test_params": { - "global_params": {}, - "engine_params": {} + "global_params": { + "ref_name": "GRCh38" + }, + "engine_params": { + "pacbio-hpc": { + "resources_file_path": "/pbi/vast-collections/appslabht/cromwell_tests/humanwgs", + "datasets_file_path": "/pbi/vast-collections/appslabht/cromwell_tests/humanwgs/hifi-wdl-resources-v2.0.0", + "ref_fasta": "/pbi/vast-collections/appslabht/cromwell_tests/humanwgs/hifi-wdl-resources-v2.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.fasta", + "ref_index": "/pbi/vast-collections/appslabht/cromwell_tests/humanwgs/hifi-wdl-resources-v2.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai", + "default_runtime_attributes": { + "backend": "HPC", + "preemptible_tries": 0, + "max_retries": 0, + "zones": "", + "gpuType": "ampere", + "container_registry": "quay.io/pacbio" + }, + "on_demand_runtime_attributes": { + "backend": "HPC", + "preemptible_tries": 0, + "max_retries": 0, + "zones": "", + "gpuType": "ampere", + "container_registry": "quay.io/pacbio" + } + } + } } } \ No newline at end of file diff --git a/workflows/family.wdl b/workflows/family.wdl index e9c86fa..7c86be9 100644 --- a/workflows/family.wdl +++ b/workflows/family.wdl @@ -400,6 +400,6 @@ workflow humanwgs_family { # workflow metadata String workflow_name = "humanwgs_family" - String workflow_version = "v2.0.5" + if defined(debug_version) then "~{"-" + debug_version}" else "" + String workflow_version = "v2.0.7" + if defined(debug_version) then "~{"-" + debug_version}" else "" } } \ No newline at end of file diff --git a/workflows/singleton.wdl b/workflows/singleton.wdl index 374ff21..ae3cdb8 100644 --- a/workflows/singleton.wdl +++ b/workflows/singleton.wdl @@ -332,6 +332,6 @@ workflow humanwgs_singleton { # workflow metadata String workflow_name = "humanwgs_family" - String workflow_version = "v2.0.5" + if defined(debug_version) then "~{"-" + debug_version}" else "" + String workflow_version = "v2.0.7" + if defined(debug_version) then "~{"-" + debug_version}" else "" } } diff --git a/workflows/wdl-common b/workflows/wdl-common index 34fa547..60e9eb5 160000 --- a/workflows/wdl-common +++ b/workflows/wdl-common @@ -1 +1 @@ -Subproject commit 34fa5471870a0eb7bcb7c4fd6667faecb34b83dd +Subproject commit 60e9eb5c798b6d35dc26fe8561423cf1dab193bd