Updated several outputs keys and filenames for clarity and better fil…

…e sorting.
PacificBiosciences · Oct 15, 2024 · 54fb5c6 · 54fb5c6
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commit 54fb5c6
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Showing 6 changed files with 64 additions and 63 deletions.
diff --git a/docs/family.md b/docs/family.md
@@ -145,10 +145,10 @@ The `Sample` struct contains sample specific data and metadata. The struct has t
 | Array\[File\] | small_variant_gvcf | Small variant GVCF | Can be used for joint-calling. |
 | Array\[File\] | small_variant_gvcf_index |  |  |
 | Array\[File\] | small_variant_stats | Small variant stats | Generated by `bcftools stats`. |
-| Array\[String\] | stat_SNV_count | SNV count | (PASS variants) |
-| Array\[String\] | stat_INDEL_count | INDEL count | (PASS variants) |
-| Array\[String\] | stat_TSTV_ratio | Ts/Tv ratio | (PASS variants) |
-| Array\[String\] | stat_HETHOM_ratio | Het/Hom ratio | (PASS variants) |
+| Array\[String\] | stat_small_variant_SNV_count | SNV count | (PASS variants) |
+| Array\[String\] | stat_small_variant_INDEL_count | INDEL count | (PASS variants) |
+| Array\[String\] | stat_small_variant_TSTV_ratio | Ts/Tv ratio | (PASS variants) |
+| Array\[String\] | stat_small_variant_HETHOM_ratio | Het/Hom ratio | (PASS variants) |
 | File? | joint_small_variants_vcf | Joint-called small variant VCF |  |
 | File? | joint_small_variants_vcf_index |  |  |
 
@@ -222,9 +222,9 @@ The `Sample` struct contains sample specific data and metadata. The struct has t
 | Array\[File\] | cpg_hap1_bw | CpG hap1 BigWig |  |
 | Array\[File\] | cpg_hap2_bw | CpG hap2 BigWig |  |
 | Array\[File\] | cpg_combined_bw | CpG combined BigWig |  |
-| Array\[String\] | stat_hap1_cpg_count | Hap1 CpG count |  |
-| Array\[String\] | stat_hap2_cpg_count | Hap2 CpG count |  |
-| Array\[String\] | stat_combined_cpg_count | Combined CpG count |  |
+| Array\[String\] | stat_cpg_hap1_count | Hap1 CpG count |  |
+| Array\[String\] | stat_cpg_hap2_count | Hap2 CpG count |  |
+| Array\[String\] | stat_cpg_combined_count | Combined CpG count |  |
 
 ### PGx Typing
 

diff --git a/docs/singleton.md b/docs/singleton.md
@@ -110,10 +110,10 @@ flowchart TD
 | File | small_variant_gvcf | Small variant GVCF | Can be used for joint-calling. |
 | File | small_variant_gvcf_index |  |  |
 | File | small_variant_stats | Small variant stats | Generated by `bcftools stats`. |
-| String | stat_SNV_count | SNV count | (PASS variants) |
-| String | stat_INDEL_count | INDEL count | (PASS variants) |
-| String | stat_TSTV_ratio | Ts/Tv ratio | (PASS variants) |
-| String | stat_HETHOM_ratio | Het/Hom ratio | (PASS variants) |
+| String | stat_small_variant_SNV_count | SNV count | (PASS variants) |
+| String | stat_small_variant_INDEL_count | INDEL count | (PASS variants) |
+| String | stat_small_variant_TSTV_ratio | Ts/Tv ratio | (PASS variants) |
+| String | stat_small_variant_HETHOM_ratio | Het/Hom ratio | (PASS variants) |
 
 ### Structural Variants (≥50 bp)
 
@@ -183,9 +183,9 @@ flowchart TD
 | File | cpg_hap1_bw | CpG hap1 BigWig |  |
 | File | cpg_hap2_bw | CpG hap2 BigWig |  |
 | File | cpg_combined_bw | CpG combined BigWig |  |
-| String | stat_hap1_cpg_count | Hap1 CpG count |  |
-| String | stat_hap2_cpg_count | Hap2 CpG count |  |
-| String | stat_combined_cpg_count | Combined CpG count |  |
+| String | stat_cpg_hap1_count | Hap1 CpG count |  |
+| String | stat_cpg_hap2_count | Hap2 CpG count |  |
+| String | stat_cpg_combined_count | Combined CpG count |  |
 
 ### PGx Typing
 

diff --git a/workflows/downstream/downstream.wdl b/workflows/downstream/downstream.wdl
@@ -143,7 +143,8 @@ workflow downstream {
   }
 
   call Pharmcat.pharmcat {
-    input: 
+    input:
+      sample_id                  = sample_id,
       haplotagged_bam            = hiphase.haplotagged_bam,
       haplotagged_bam_index      = hiphase.haplotagged_bam_index,
       phased_vcf                 = hiphase.phased_vcfs[0],

diff --git a/workflows/family.wdl b/workflows/family.wdl
@@ -272,9 +272,9 @@ workflow humanwgs_family {
     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_hap1_cpg_count     = downstream.stat_hap1_cpg_count
-    Array[String] stat_hap2_cpg_count     = downstream.stat_hap2_cpg_count
-    Array[String] stat_combined_cpg_count = downstream.stat_combined_cpg_count
+    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
 
     # sv outputs
     Array[File] phased_sv_vcf       = downstream.phased_sv_vcf
@@ -294,13 +294,13 @@ 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[String] stat_SNV_count    = downstream.stat_SNV_count
-    Array[String] stat_INDEL_count  = downstream.stat_INDEL_count
-    Array[String] stat_TSTV_ratio   = downstream.stat_TSTV_ratio
-    Array[String] stat_HETHOM_ratio = downstream.stat_HETHOM_ratio
+    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
 
     # trgt outputs
     Array[File] phased_trgt_vcf             = downstream.phased_trgt_vcf
@@ -317,7 +317,7 @@ workflow humanwgs_family {
     Array[File] paraphase_realigned_bam_index = upstream.paraphase_realigned_bam_index
     Array[File?] paraphase_vcfs               = upstream.paraphase_vcfs
 
-    # per sample ficnv outputs
+    # 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

diff --git a/workflows/singleton.wdl b/workflows/singleton.wdl
@@ -213,9 +213,9 @@ workflow humanwgs_singleton {
     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_hap1_cpg_count     = downstream.stat_hap1_cpg_count
-    String stat_hap2_cpg_count     = downstream.stat_hap2_cpg_count
-    String stat_combined_cpg_count = downstream.stat_combined_cpg_count
+    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
 
     # sv outputs
     File phased_sv_vcf       = downstream.phased_sv_vcf
@@ -235,13 +235,13 @@ workflow humanwgs_singleton {
     File small_variant_gvcf_index       = upstream.small_variant_gvcf_index
 
     # small variant stats
-    File   small_variant_stats = downstream.small_variant_stats
-    File   bcftools_roh_out    = downstream.bcftools_roh_out
-    File   bcftools_roh_bed    = downstream.bcftools_roh_bed
-    String stat_SNV_count      = downstream.stat_SNV_count
-    String stat_INDEL_count    = downstream.stat_INDEL_count
-    String stat_TSTV_ratio     = downstream.stat_TSTV_ratio
-    String stat_HETHOM_ratio   = downstream.stat_HETHOM_ratio
+    File   small_variant_stats             = downstream.small_variant_stats
+    File   bcftools_roh_out                = downstream.bcftools_roh_out
+    File   bcftools_roh_bed                = downstream.bcftools_roh_bed
+    String stat_small_variant_SNV_count    = downstream.stat_SNV_count
+    String stat_small_variant_INDEL_count  = downstream.stat_INDEL_count
+    String stat_small_variant_TSTV_ratio   = downstream.stat_TSTV_ratio
+    String stat_small_variant_HETHOM_ratio = downstream.stat_HETHOM_ratio
 
     # trgt outputs
     File   phased_trgt_vcf           = downstream.phased_trgt_vcf
@@ -259,15 +259,15 @@ workflow humanwgs_singleton {
     File? paraphase_vcfs                = upstream.paraphase_vcfs
 
     # per sample cnv outputs
-    File cnv_vcf              = upstream.cnv_vcf
-    File cnv_vcf_index        = upstream.cnv_vcf_index
-    File cnv_copynum_bedgraph = upstream.cnv_copynum_bedgraph
-    File cnv_depth_bw         = upstream.cnv_depth_bw
-    File cnv_maf_bw           = upstream.cnv_maf_bw
-    String stat_cnv_DUP_count = upstream.stat_cnv_DUP_count
-    String stat_cnv_DEL_count = upstream.stat_cnv_DEL_count
-    String stat_cnv_DUP_sum   = upstream.stat_cnv_DUP_sum
-    String stat_cnv_DEL_sum   = upstream.stat_cnv_DEL_sum
+    File   cnv_vcf              = upstream.cnv_vcf
+    File   cnv_vcf_index        = upstream.cnv_vcf_index
+    File   cnv_copynum_bedgraph = upstream.cnv_copynum_bedgraph
+    File   cnv_depth_bw         = upstream.cnv_depth_bw
+    File   cnv_maf_bw           = upstream.cnv_maf_bw
+    String stat_cnv_DUP_count   = upstream.stat_cnv_DUP_count
+    String stat_cnv_DEL_count   = upstream.stat_cnv_DEL_count
+    String stat_cnv_DUP_sum     = upstream.stat_cnv_DUP_sum
+    String stat_cnv_DEL_sum     = upstream.stat_cnv_DEL_sum
 
     # PGx outputs
     File pbstarphase_json        = downstream.pbstarphase_json

diff --git a/workflows/tertiary/tertiary.wdl b/workflows/tertiary/tertiary.wdl
@@ -36,31 +36,31 @@ workflow tertiary_analysis {
     default_runtime_attributes: {
       name: "Runtime attribute structure"
     }
-    filtered_small_variant_vcf: {
+    small_variant_filtered_vcf: {
       name: "Filtered and annotated small variant VCF"
     }
-    filtered_small_variant_vcf_index: {
+    small_variant_filtered_vcf_index: {
       name: "Filtered and annotated small variant VCF index"
     }
-    filtered_small_variant_tsv: {
+    small_variant_filtered_tsv: {
       name: "Filtered and annotated small variant TSV"
     }
-    compound_het_small_variant_vcf: {
+    small_variant_compound_het_vcf: {
       name: "Filtered and annotated compound heterozygous small variant VCF"
     }
-    compound_het_small_variant_vcf_index: {
+    small_variant_compound_het_vcf_index: {
       name: "Filtered and annotated compound heterozygous small variant VCF index"
     }
-    compound_het_small_variant_tsv: {
+    small_variant_compound_het_tsv: {
       name: "Filtered and annotated compound heterozygous small variant TSV"
     }
-    filtered_svpack_vcf: {
+    sv_filtered_vcf: {
       name: "Filtered and annotated structural variant VCF"
     }
-    filtered_svpack_vcf_index: {
+    sv_filtered_vcf_index: {
       name: "Filtered and annotated structural variant VCF index"
     }
-    filtered_svpack_tsv: {
+    sv_filtered_tsv: {
       name: "Filtered and annotated structural variant TSV"
     }
   }
@@ -166,17 +166,17 @@ workflow tertiary_analysis {
   }
 
   output {
-    File filtered_small_variant_vcf       = slivar_small_variant.filtered_vcf
-    File filtered_small_variant_vcf_index = slivar_small_variant.filtered_vcf_index
-    File filtered_small_variant_tsv       = slivar_small_variant.filtered_tsv
+    File small_variant_filtered_vcf       = slivar_small_variant.filtered_vcf
+    File small_variant_filtered_vcf_index = slivar_small_variant.filtered_vcf_index
+    File small_variant_filtered_tsv       = slivar_small_variant.filtered_tsv
 
-    File compound_het_small_variant_vcf       = slivar_small_variant.compound_het_vcf
-    File compound_het_small_variant_vcf_index = slivar_small_variant.compound_het_vcf_index
-    File compound_het_small_variant_tsv       = slivar_small_variant.compound_het_tsv
+    File small_variant_compound_het_vcf       = slivar_small_variant.compound_het_vcf
+    File small_variant_compound_het_vcf_index = slivar_small_variant.compound_het_vcf_index
+    File small_variant_compound_het_tsv       = slivar_small_variant.compound_het_tsv
 
-    File filtered_svpack_vcf       = svpack_filter_annotated.svpack_vcf
-    File filtered_svpack_vcf_index = svpack_filter_annotated.svpack_vcf_index
-    File filtered_svpack_tsv       = slivar_svpack_tsv.svpack_tsv
+    File sv_filtered_vcf       = svpack_filter_annotated.svpack_vcf
+    File sv_filtered_vcf_index = svpack_filter_annotated.svpack_vcf_index
+    File sv_filtered_tsv       = slivar_svpack_tsv.svpack_tsv
   }
 }