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Merge pull request #176 from PacificBiosciences/fix/remove_starphase_…
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…nocalls

Gracefully handle low depth samples with StarPhase/PharmCAT
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@williamrowell
williamrowell authored Dec 20, 2024
2 parents 79e2640 + 34466b0 commit 9c55fc5
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Showing 5 changed files with 126 additions and 85 deletions.
45 changes: 43 additions & 2 deletions wdl-ci.config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2390,7 +2390,7 @@
},
"filter_preprocessed_vcf": {
"key": "filter_preprocessed_vcf",
"digest": "63mmofid6b46ugrq6hhmlpdc6htd767o",
"digest": "4jjtxpixe6gq6p3v7lnuyxhlzottg2ib",
"tests": [
{
"inputs": {
Expand All @@ -2415,7 +2415,7 @@
},
"run_pharmcat": {
"key": "run_pharmcat",
"digest": "bpvbkvx6hsvzy7a3mymzjrwqvgxdrmj7",
"digest": "nsabvlc6qz2u6y7ikis4pa4oljfanewp",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -2457,6 +2457,47 @@
]
}
}
},
{
"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.NO_READS.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/NO_READS/HG002.pharmcat.match.json",
"test_tasks": [
"compare_file_basename",
"check_json"
]
},
"pharmcat_phenotype_json": {
"value": "${resources_file_path}/run_pharmcat/output/NO_READS/HG002.pharmcat.phenotype.json",
"test_tasks": [
"compare_file_basename",
"check_json"
]
},
"pharmcat_report_html": {
"value": "${resources_file_path}/run_pharmcat/output/NO_READS/HG002.pharmcat.report.html",
"test_tasks": [
"compare_file_basename",
"check_html"
]
},
"pharmcat_report_json": {
"value": "${resources_file_path}/run_pharmcat/output/NO_READS/HG002.pharmcat.report.json",
"test_tasks": [
"compare_file_basename",
"check_json"
]
}
}
}
]
}
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26 changes: 13 additions & 13 deletions workflows/downstream/downstream.wdl
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Expand Up @@ -198,15 +198,15 @@ workflow downstream {
String stat_sv_BND_count = sv_stats.stat_sv_BND_count

# cpg_pileup outputs
File? cpg_combined_bed = cpg_pileup.combined_bed
File? cpg_combined_bed_index = cpg_pileup.combined_bed_index
File? cpg_hap1_bed = cpg_pileup.hap1_bed
File? cpg_hap1_bed_index = cpg_pileup.hap1_bed_index
File? cpg_hap2_bed = cpg_pileup.hap2_bed
File? cpg_hap2_bed_index = cpg_pileup.hap2_bed_index
File? cpg_combined_bw = cpg_pileup.combined_bw
File? cpg_hap1_bw = cpg_pileup.hap1_bw
File? cpg_hap2_bw = cpg_pileup.hap2_bw
File? cpg_combined_bed = cpg_pileup.combined_bed
File? cpg_combined_bed_index = cpg_pileup.combined_bed_index
File? cpg_hap1_bed = cpg_pileup.hap1_bed
File? cpg_hap1_bed_index = cpg_pileup.hap1_bed_index
File? cpg_hap2_bed = cpg_pileup.hap2_bed
File? cpg_hap2_bed_index = cpg_pileup.hap2_bed_index
File? cpg_combined_bw = cpg_pileup.combined_bw
File? cpg_hap1_bw = cpg_pileup.hap1_bw
File? cpg_hap2_bw = cpg_pileup.hap2_bw
String stat_hap1_cpg_count = cpg_pileup.stat_hap1_cpg_count
String stat_hap2_cpg_count = cpg_pileup.stat_hap2_cpg_count
String stat_combined_cpg_count = cpg_pileup.stat_combined_cpg_count
Expand All @@ -215,9 +215,9 @@ workflow downstream {
File pbstarphase_json = pbstarphase_diplotype.out_json

# pharmcat and pangu outputs
File pharmcat_match_json = pharmcat.pharmcat_match_json
File pharmcat_phenotype_json = pharmcat.pharmcat_phenotype_json
File pharmcat_report_html = pharmcat.pharmcat_report_html
File pharmcat_report_json = pharmcat.pharmcat_report_json
File? pharmcat_match_json = pharmcat.pharmcat_match_json
File? pharmcat_phenotype_json = pharmcat.pharmcat_phenotype_json
File? pharmcat_report_html = pharmcat.pharmcat_report_html
File? pharmcat_report_json = pharmcat.pharmcat_report_json
}
}
110 changes: 55 additions & 55 deletions workflows/family.wdl
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Expand Up @@ -271,48 +271,48 @@ workflow humanwgs_family {
File stats_file = consolidate_stats.output_tsv

# bam stats
Array[File] bam_stats = upstream.read_length_and_quality
Array[File] read_length_plot = upstream.read_length_plot
Array[File?] read_quality_plot = upstream.read_quality_plot
Array[File] bam_stats = upstream.read_length_and_quality
Array[File] read_length_plot = upstream.read_length_plot
Array[File?] read_quality_plot = upstream.read_quality_plot
Array[String] stat_num_reads = upstream.stat_num_reads
Array[String] stat_read_length_mean = upstream.stat_read_length_mean
Array[String] stat_read_length_median = upstream.stat_read_length_median
Array[String] stat_read_quality_mean = upstream.stat_read_quality_mean
Array[String] stat_read_quality_median = upstream.stat_read_quality_median

# merged, haplotagged alignments
Array[File] merged_haplotagged_bam = downstream.merged_haplotagged_bam
Array[File] merged_haplotagged_bam_index = downstream.merged_haplotagged_bam_index
Array[String] stat_mapped_read_count = downstream.stat_mapped_read_count
Array[String] stat_mapped_percent = downstream.stat_mapped_percent
Array[File] mapq_distribution_plot = downstream.mapq_distribution_plot
Array[File] mg_distribution_plot = downstream.mg_distribution_plot
Array[File] merged_haplotagged_bam = downstream.merged_haplotagged_bam
Array[File] merged_haplotagged_bam_index = downstream.merged_haplotagged_bam_index
Array[String] stat_mapped_read_count = downstream.stat_mapped_read_count
Array[String] stat_mapped_percent = downstream.stat_mapped_percent
Array[File] mapq_distribution_plot = downstream.mapq_distribution_plot
Array[File] mg_distribution_plot = downstream.mg_distribution_plot

# mosdepth outputs
Array[File] mosdepth_summary = upstream.mosdepth_summary
Array[File] mosdepth_region_bed = upstream.mosdepth_region_bed
Array[File] mosdepth_region_bed_index = upstream.mosdepth_region_bed_index
Array[File] mosdepth_depth_distribution_plot = upstream.mosdepth_depth_distribution_plot
Array[String] stat_mean_depth = upstream.stat_mean_depth
Array[String] inferred_sex = upstream.inferred_sex
Array[File] mosdepth_summary = upstream.mosdepth_summary
Array[File] mosdepth_region_bed = upstream.mosdepth_region_bed
Array[File] mosdepth_region_bed_index = upstream.mosdepth_region_bed_index
Array[File] mosdepth_depth_distribution_plot = upstream.mosdepth_depth_distribution_plot
Array[String] stat_mean_depth = upstream.stat_mean_depth
Array[String] inferred_sex = upstream.inferred_sex

# phasing stats
Array[File] phase_stats = downstream.phase_stats
Array[File] phase_blocks = downstream.phase_blocks
Array[File] phase_haplotags = downstream.phase_haplotags
Array[File] phase_stats = downstream.phase_stats
Array[File] phase_blocks = downstream.phase_blocks
Array[File] phase_haplotags = downstream.phase_haplotags
Array[String] stat_phased_basepairs = downstream.stat_phased_basepairs
Array[String] stat_phase_block_ng50 = downstream.stat_phase_block_ng50

# cpg_pileup outputs
Array[File?] cpg_combined_bed = downstream.cpg_combined_bed
Array[File?] cpg_combined_bed_index = downstream.cpg_combined_bed_index
Array[File?] cpg_hap1_bed = downstream.cpg_hap1_bed
Array[File?] cpg_hap1_bed_index = downstream.cpg_hap1_bed_index
Array[File?] cpg_hap2_bed = downstream.cpg_hap2_bed
Array[File?] cpg_hap2_bed_index = downstream.cpg_hap2_bed_index
Array[File?] cpg_combined_bw = downstream.cpg_combined_bw
Array[File?] cpg_hap1_bw = downstream.cpg_hap1_bw
Array[File?] cpg_hap2_bw = downstream.cpg_hap2_bw
Array[File?] cpg_combined_bed = downstream.cpg_combined_bed
Array[File?] cpg_combined_bed_index = downstream.cpg_combined_bed_index
Array[File?] cpg_hap1_bed = downstream.cpg_hap1_bed
Array[File?] cpg_hap1_bed_index = downstream.cpg_hap1_bed_index
Array[File?] cpg_hap2_bed = downstream.cpg_hap2_bed
Array[File?] cpg_hap2_bed_index = downstream.cpg_hap2_bed_index
Array[File?] cpg_combined_bw = downstream.cpg_combined_bw
Array[File?] cpg_hap1_bw = downstream.cpg_hap1_bw
Array[File?] cpg_hap2_bw = downstream.cpg_hap2_bw
Array[String] stat_cpg_hap1_count = downstream.stat_hap1_cpg_count
Array[String] stat_cpg_hap2_count = downstream.stat_hap2_cpg_count
Array[String] stat_cpg_combined_count = downstream.stat_combined_cpg_count
Expand All @@ -335,48 +335,48 @@ workflow humanwgs_family {
Array[File] small_variant_gvcf_index = upstream.small_variant_gvcf_index

# small variant stats
Array[File] small_variant_stats = downstream.small_variant_stats
Array[File] bcftools_roh_out = downstream.bcftools_roh_out
Array[File] bcftools_roh_bed = downstream.bcftools_roh_bed
Array[File] small_variant_stats = downstream.small_variant_stats
Array[File] bcftools_roh_out = downstream.bcftools_roh_out
Array[File] bcftools_roh_bed = downstream.bcftools_roh_bed
Array[String] stat_small_variant_SNV_count = downstream.stat_SNV_count
Array[String] stat_small_variant_INDEL_count = downstream.stat_INDEL_count
Array[String] stat_small_variant_TSTV_ratio = downstream.stat_TSTV_ratio
Array[String] stat_small_variant_HETHOM_ratio = downstream.stat_HETHOM_ratio
Array[File] snv_distribution_plot = downstream.snv_distribution_plot
Array[File] indel_distribution_plot = downstream.indel_distribution_plot
Array[File] snv_distribution_plot = downstream.snv_distribution_plot
Array[File] indel_distribution_plot = downstream.indel_distribution_plot

# trgt outputs
Array[File] phased_trgt_vcf = downstream.phased_trgt_vcf
Array[File] phased_trgt_vcf_index = downstream.phased_trgt_vcf_index
Array[File] trgt_spanning_reads = upstream.trgt_spanning_reads
Array[File] trgt_spanning_reads_index = upstream.trgt_spanning_reads_index
Array[File] trgt_coverage_dropouts = upstream.trgt_coverage_dropouts
Array[File] phased_trgt_vcf = downstream.phased_trgt_vcf
Array[File] phased_trgt_vcf_index = downstream.phased_trgt_vcf_index
Array[File] trgt_spanning_reads = upstream.trgt_spanning_reads
Array[File] trgt_spanning_reads_index = upstream.trgt_spanning_reads_index
Array[File] trgt_coverage_dropouts = upstream.trgt_coverage_dropouts
Array[String] stat_trgt_genotyped_count = upstream.stat_trgt_genotyped_count
Array[String] stat_trgt_uncalled_count = upstream.stat_trgt_uncalled_count

# paraphase outputs
Array[File] paraphase_output_json = upstream.paraphase_output_json
Array[File] paraphase_realigned_bam = upstream.paraphase_realigned_bam
Array[File] paraphase_realigned_bam_index = upstream.paraphase_realigned_bam_index
Array[File?] paraphase_vcfs = upstream.paraphase_vcfs
Array[File] paraphase_output_json = upstream.paraphase_output_json
Array[File] paraphase_realigned_bam = upstream.paraphase_realigned_bam
Array[File] paraphase_realigned_bam_index = upstream.paraphase_realigned_bam_index
Array[File?] paraphase_vcfs = upstream.paraphase_vcfs

# per sample cnv outputs
Array[File] cnv_vcf = upstream.cnv_vcf
Array[File] cnv_vcf_index = upstream.cnv_vcf_index
Array[File] cnv_copynum_bedgraph = upstream.cnv_copynum_bedgraph
Array[File] cnv_depth_bw = upstream.cnv_depth_bw
Array[File] cnv_maf_bw = upstream.cnv_maf_bw
Array[String] stat_cnv_DUP_count = upstream.stat_cnv_DUP_count
Array[String] stat_cnv_DEL_count = upstream.stat_cnv_DEL_count
Array[String] stat_cnv_DUP_sum = upstream.stat_cnv_DUP_sum
Array[String] stat_cnv_DEL_sum = upstream.stat_cnv_DEL_sum
Array[File] cnv_vcf = upstream.cnv_vcf
Array[File] cnv_vcf_index = upstream.cnv_vcf_index
Array[File] cnv_copynum_bedgraph = upstream.cnv_copynum_bedgraph
Array[File] cnv_depth_bw = upstream.cnv_depth_bw
Array[File] cnv_maf_bw = upstream.cnv_maf_bw
Array[String] stat_cnv_DUP_count = upstream.stat_cnv_DUP_count
Array[String] stat_cnv_DEL_count = upstream.stat_cnv_DEL_count
Array[String] stat_cnv_DUP_sum = upstream.stat_cnv_DUP_sum
Array[String] stat_cnv_DEL_sum = upstream.stat_cnv_DEL_sum

# PGx outputs
Array[File] pbstarphase_json = downstream.pbstarphase_json
Array[File] pharmcat_match_json = downstream.pharmcat_match_json
Array[File] pharmcat_phenotype_json = downstream.pharmcat_phenotype_json
Array[File] pharmcat_report_html = downstream.pharmcat_report_html
Array[File] pharmcat_report_json = downstream.pharmcat_report_json
Array[File] pbstarphase_json = downstream.pbstarphase_json
Array[File?] pharmcat_match_json = downstream.pharmcat_match_json
Array[File?] pharmcat_phenotype_json = downstream.pharmcat_phenotype_json
Array[File?] pharmcat_report_html = downstream.pharmcat_report_html
Array[File?] pharmcat_report_json = downstream.pharmcat_report_json

# joint call outputs
File? joint_small_variants_vcf = merge_small_variant_vcfs.merged_vcf
Expand Down
28 changes: 14 additions & 14 deletions workflows/singleton.wdl
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Expand Up @@ -244,15 +244,15 @@ workflow humanwgs_singleton {
String stat_phase_block_ng50 = downstream.stat_phase_block_ng50

# cpg_pileup outputs
File? cpg_combined_bed = downstream.cpg_combined_bed
File? cpg_combined_bed_index = downstream.cpg_combined_bed_index
File? cpg_hap1_bed = downstream.cpg_hap1_bed
File? cpg_hap1_bed_index = downstream.cpg_hap1_bed_index
File? cpg_hap2_bed = downstream.cpg_hap2_bed
File? cpg_hap2_bed_index = downstream.cpg_hap2_bed_index
File? cpg_combined_bw = downstream.cpg_combined_bw
File? cpg_hap1_bw = downstream.cpg_hap1_bw
File? cpg_hap2_bw = downstream.cpg_hap2_bw
File? cpg_combined_bed = downstream.cpg_combined_bed
File? cpg_combined_bed_index = downstream.cpg_combined_bed_index
File? cpg_hap1_bed = downstream.cpg_hap1_bed
File? cpg_hap1_bed_index = downstream.cpg_hap1_bed_index
File? cpg_hap2_bed = downstream.cpg_hap2_bed
File? cpg_hap2_bed_index = downstream.cpg_hap2_bed_index
File? cpg_combined_bw = downstream.cpg_combined_bw
File? cpg_hap1_bw = downstream.cpg_hap1_bw
File? cpg_hap2_bw = downstream.cpg_hap2_bw
String stat_cpg_hap1_count = downstream.stat_hap1_cpg_count
String stat_cpg_hap2_count = downstream.stat_hap2_cpg_count
String stat_cpg_combined_count = downstream.stat_combined_cpg_count
Expand Down Expand Up @@ -312,11 +312,11 @@ workflow humanwgs_singleton {
String stat_cnv_DEL_sum = upstream.stat_cnv_DEL_sum

# PGx outputs
File pbstarphase_json = downstream.pbstarphase_json
File pharmcat_match_json = downstream.pharmcat_match_json
File pharmcat_phenotype_json = downstream.pharmcat_phenotype_json
File pharmcat_report_html = downstream.pharmcat_report_html
File pharmcat_report_json = downstream.pharmcat_report_json
File pbstarphase_json = downstream.pbstarphase_json
File? pharmcat_match_json = downstream.pharmcat_match_json
File? pharmcat_phenotype_json = downstream.pharmcat_phenotype_json
File? pharmcat_report_html = downstream.pharmcat_report_html
File? pharmcat_report_json = downstream.pharmcat_report_json

# tertiary analysis outputs
File? pedigree = write_ped_phrank.pedigree
Expand Down
2 changes: 1 addition & 1 deletion workflows/wdl-common
Submodule wdl-common updated 1 files
+26 −22 wdl/workflows/pharmcat/pharmcat.wdl

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