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Next minor release. #174

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merged 25 commits into from
Jan 10, 2025
Merged

Next minor release. #174

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4f8d071
Support for BAMs that lack basemods.
williamrowell Dec 9, 2024
85472e8
update wdl-ci config file after successful tests
github-actions[bot] Dec 9, 2024
342d259
Support input without rq values.
williamrowell Dec 9, 2024
8445aed
update wdl-ci config file after successful tests
github-actions[bot] Dec 10, 2024
ecdbf3e
Added merge_bam_stats test for sample with no rq.
williamrowell Dec 10, 2024
381313b
update wdl-ci config file after successful tests
github-actions[bot] Dec 10, 2024
71a1115
Updated to TRGT v1.4.1.
williamrowell Nov 27, 2024
a0504ae
Address trgt OOM errors when using catalogs with very low complexity …
williamrowell Dec 13, 2024
b7934ed
update wdl-ci config file after successful tests
github-actions[bot] Dec 17, 2024
c3734ab
Merge pull request #173 from PacificBiosciences/feature/trgt-v1.4.1
williamrowell Dec 17, 2024
108657f
Update to pbmm2 v1.16.99 prerelease.
williamrowell Dec 18, 2024
d959399
update wdl-ci config file after successful tests
github-actions[bot] Dec 18, 2024
79e2640
Merge pull request #177 from PacificBiosciences/fix/pbmm2-1.16.99
williamrowell Dec 20, 2024
a6a0565
Filter `NO_READS` no-call lines from StarPhase input to PharmCAT.
williamrowell Dec 18, 2024
0e6292a
update wdl-ci config file after successful tests
github-actions[bot] Dec 18, 2024
21ab0ef
Only attempt to run PharmCAT if at least one PharmCAT region has dept…
williamrowell Dec 18, 2024
d291a4d
update wdl-ci config file after successful tests
github-actions[bot] Dec 18, 2024
8e62d96
Added test for exclusion of NO_READS.
williamrowell Dec 18, 2024
1b76849
update wdl-ci config file after successful tests
github-actions[bot] Dec 18, 2024
34466b0
update wdl-ci config file after successful tests
github-actions[bot] Dec 18, 2024
9c55fc5
Merge pull request #176 from PacificBiosciences/fix/remove_starphase_…
williamrowell Dec 20, 2024
91c07c7
Update trgt coverage_dropouts task to use trgt v1.4.1 docker image.
williamrowell Jan 10, 2025
9455956
Update docs.
williamrowell Jan 10, 2025
507d6bf
Update documentation for #178
williamrowell Jan 10, 2025
24ce228
update wdl-ci config file after successful tests
github-actions[bot] Jan 10, 2025
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Only attempt to run PharmCAT if at least one PharmCAT region has dept… 
…h > pharmcat_min_coverage

- make PharmCAT outputs optional
  • Loading branch information
@williamrowell
williamrowell committed Dec 20, 2024
commit 21ab0ef650017e04c5d74a8e370cc1cafd840adf
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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Original file line number Diff line number Diff line change
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