PacificBiosciences · williamrowell · Dec 9, 2024 · Dec 9, 2024 · Dec 9, 2024 · Dec 10, 2024
diff --git a/docs/family.md b/docs/family.md
@@ -119,7 +119,7 @@ The `Sample` struct contains sample specific data and metadata. The struct has t
 | File | stats_file | Table of summary statistics |  |
 | Array\[File\] | bam_stats | BAM stats | Per-read length and read-quality |
 | Array\[File\] | read_length_plot | Read length plot |  |
-| Array\[File\] | read_quality_plot | Read quality plot |  |
+| Array\[File?\] | read_quality_plot | Read quality plot |  |
 | Array\[File\] | merged_haplotagged_bam | Merged, haplotagged alignments | Includes unmapped reads |
 | Array\[File\] | merged_haplotagged_bam_index |  |  |
 | Array\[File\] | mosdepth_summary | Summary of aligned read depth. |  |
@@ -223,15 +223,15 @@ The `Sample` struct contains sample specific data and metadata. The struct has t
 
 | Type | Name | Description | Notes |
 | ---- | ---- | ----------- | ----- |
-| Array\[File\] | cpg_hap1_bed | CpG hap1 BED |  |
-| Array\[File\] | cpg_hap1_bed_index |  |  |
-| Array\[File\] | cpg_hap2_bed | CpG hap2 BED |  |
-| Array\[File\] | cpg_hap2_bed_index |  |  |
-| Array\[File\] | cpg_combined_bed | CpG combined BED |  |
-| Array\[File\] | cpg_combined_bed_index |  |  |
-| 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\[File?\] | cpg_hap1_bed | CpG hap1 BED |  |
+| Array\[File?\] | cpg_hap1_bed_index |  |  |
+| Array\[File?\] | cpg_hap2_bed | CpG hap2 BED |  |
+| Array\[File?\] | cpg_hap2_bed_index |  |  |
+| Array\[File?\] | cpg_combined_bed | CpG combined BED |  |
+| Array\[File?\] | cpg_combined_bed_index |  |  |
+| 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_cpg_hap1_count | Hap1 CpG count |  |
 | Array\[String\] | stat_cpg_hap2_count | Hap2 CpG count |  |
 | Array\[String\] | stat_cpg_combined_count | Combined CpG count |  |

diff --git a/docs/singleton.md b/docs/singleton.md
@@ -84,7 +84,7 @@ flowchart TD
 | File | stats_file | Table of summary statistics |  |
 | File | bam_stats | BAM stats | Per-read length and read-quality |
 | File | read_length_plot | Read length plot |  |
-| File | read_quality_plot | Read quality plot |  |
+| File? | read_quality_plot | Read quality plot |  |
 | File | merged_haplotagged_bam | Merged, haplotagged alignments | Includes unmapped reads |
 | File | merged_haplotagged_bam_index |  |  |
 | File | mosdepth_summary | Summary of aligned read depth. |  |
@@ -182,15 +182,15 @@ flowchart TD
 
 | Type | Name | Description | Notes |
 | ---- | ---- | ----------- | ----- |
-| File | cpg_hap1_bed | CpG hap1 BED |  |
-| File | cpg_hap1_bed_index |  |  |
-| File | cpg_hap2_bed | CpG hap2 BED |  |
-| File | cpg_hap2_bed_index |  |  |
-| File | cpg_combined_bed | CpG combined BED |  |
-| File | cpg_combined_bed_index |  |  |
-| File | cpg_hap1_bw | CpG hap1 BigWig |  |
-| File | cpg_hap2_bw | CpG hap2 BigWig |  |
-| File | cpg_combined_bw | CpG combined BigWig |  |
+| File? | cpg_hap1_bed | CpG hap1 BED |  |
+| File? | cpg_hap1_bed_index |  |  |
+| File? | cpg_hap2_bed | CpG hap2 BED |  |
+| File? | cpg_hap2_bed_index |  |  |
+| File? | cpg_combined_bed | CpG combined BED |  |
+| File? | cpg_combined_bed_index |  |  |
+| File? | cpg_hap1_bw | CpG hap1 BigWig |  |
+| File? | cpg_hap2_bw | CpG hap2 BigWig |  |
+| File? | cpg_combined_bw | CpG combined BigWig |  |
 | String | stat_cpg_hap1_count | Hap1 CpG count |  |
 | String | stat_cpg_hap2_count | Hap2 CpG count |  |
 | String | stat_cpg_combined_count | Combined CpG count |  |

diff --git a/wdl-ci.config.json b/wdl-ci.config.json
@@ -586,7 +586,7 @@
       "tasks": {
         "cpg_pileup": {
           "key": "cpg_pileup",
-          "digest": "noq7e5yf5h6s2sf7lzolbgigqec4izmg",
+          "digest": "km7kr546iovkhccy3yb2ovvvdmmnmet7",
           "tests": [
             {
               "inputs": {
@@ -665,6 +665,36 @@
                   ]
                 }
               }
+            },
+            {
+              "inputs": {
+                "haplotagged_bam": "${resources_file_path}/inputs/NA19238.GRCh38.chr6_10000000_20000000.haplotagged.bam",
+                "haplotagged_bam_index": "${resources_file_path}/inputs/NA19238.GRCh38.chr6_10000000_20000000.haplotagged.bam.bai",
+                "out_prefix": "NA19238.GRCh38",
+                "ref_fasta": "${ref_fasta}",
+                "ref_index": "${ref_index}",
+                "runtime_attributes": "${default_runtime_attributes}"
+              },
+              "output_tests": {
+                "stat_hap1_cpg_count": {
+                  "value": "0",
+                  "test_tasks": [
+                    "compare_string"
+                  ]
+                },
+                "stat_hap2_cpg_count": {
+                  "value": "0",
+                  "test_tasks": [
+                    "compare_string"
+                  ]
+                },
+                "stat_combined_cpg_count": {
+                  "value": "0",
+                  "test_tasks": [
+                    "compare_string"
+                  ]
+                }
+              }
             }
           ]
         }
@@ -934,7 +964,7 @@
       "tasks": {
         "merge_bam_stats": {
           "key": "merge_bam_stats",
-          "digest": "k2zoxoqmson4rr7meogbb675w3bnj2gt",
+          "digest": "mjd6zpbxtabbulmq3kwhcx4cnubxaf74",
           "tests": [
             {
               "inputs": {
@@ -1068,6 +1098,64 @@
                   ]
                 }
               }
+            },
+            {
+              "inputs": {
+                "sample_id": "HG002",
+                "bam_stats": [
+                  "${resources_file_path}/pbmm2_align_wgs/vega_10k_no_rq/HG002.vega_10k.no_rq.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/no_rq/HG002.read_length_and_quality.tsv.gz",
+                  "test_tasks": [
+                    "compare_file_basename",
+                    "check_tab_delimited",
+                    "count_columns",
+                    "check_gzip"
+                  ]
+                },
+                "read_length_plot": {
+                  "value": "${resources_file_path}/merge_bam_stats/no_rq/HG002.read_length_histogram.png",
+                  "test_tasks": [
+                    "calculate_md5sum",
+                    "compare_file_basename",
+                    "png_validator"
+                  ]
+                },
+                "stat_num_reads": {
+                  "value": "10000",
+                  "test_tasks": [
+                    "compare_string"
+                  ]
+                },
+                "stat_read_length_mean": {
+                  "value": "21837.4",
+                  "test_tasks": [
+                    "compare_string"
+                  ]
+                },
+                "stat_read_length_median": {
+                  "value": "21385.0",
+                  "test_tasks": [
+                    "compare_string"
+                  ]
+                },
+                "stat_read_quality_mean": {
+                  "value": "nan",
+                  "test_tasks": [
+                    "compare_string"
+                  ]
+                },
+                "stat_read_quality_median": {
+                  "value": "nan",
+                  "test_tasks": [
+                    "compare_string"
+                  ]
+                }
+              }
             }
           ]
         }
@@ -1238,7 +1326,7 @@
       "tasks": {
         "pbmm2_align_wgs": {
           "key": "pbmm2_align_wgs",
-          "digest": "r2mrlrcc34hmpeetxabc7ujwfb2zzykq",
+          "digest": "lfkj5u6d6hakjxcmp3q6nzpwuz3jz5l3",
           "tests": [
             {
               "inputs": {
@@ -1352,6 +1440,34 @@
                   ]
                 }
               }
+            },
+            {
+              "inputs": {
+                "sample_id": "HG002",
+                "bam": "${resources_file_path}/inputs/vega_10k.no_rq.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": "${resources_file_path}/pbmm2_align_wgs/vega_10k_no_rq/HG002.vega_10k.no_rq.hifi_reads.GRCh38.aligned.bam",
+                  "test_tasks": [
+                    "compare_file_basename",
+                    "samtools_quickcheck"
+                  ]
+                },
+                "bam_stats": {
+                  "value": "${resources_file_path}/pbmm2_align_wgs/vega_10k_no_rq/HG002.vega_10k.no_rq.hifi_reads.read_length_and_quality.tsv.gz",
+                  "test_tasks": [
+                    "compare_file_basename",
+                    "check_tab_delimited",
+                    "count_columns",
+                    "check_gzip"
+                  ]
+                }
+              }
             }
           ]
         }
@@ -1562,7 +1678,7 @@
       "tasks": {
         "trgt": {
           "key": "trgt",
-          "digest": "rpcfzfr5reqxv7jbtfncu6etivzxvgs2",
+          "digest": "37d5grkookrgta6rwpmlrce3zkjavpmy",
           "tests": [
             {
               "inputs": {
@@ -1651,7 +1767,7 @@
         },
         "trgt_merge": {
           "key": "trgt_merge",
-          "digest": "cmdcqkqrcfpn2eoczxfwhs6zqhalzdtt",
+          "digest": "ljvpgmkt7sfdwpm64dqllrphd23ols56",
           "tests": [
             {
               "inputs": {
@@ -2274,7 +2390,7 @@
         },
         "filter_preprocessed_vcf": {
           "key": "filter_preprocessed_vcf",
-          "digest": "63mmofid6b46ugrq6hhmlpdc6htd767o",
+          "digest": "4jjtxpixe6gq6p3v7lnuyxhlzottg2ib",
           "tests": [
             {
               "inputs": {
@@ -2299,7 +2415,7 @@
         },
         "run_pharmcat": {
           "key": "run_pharmcat",
-          "digest": "bpvbkvx6hsvzy7a3mymzjrwqvgxdrmj7",
+          "digest": "nsabvlc6qz2u6y7ikis4pa4oljfanewp",
           "tests": [
             {
               "inputs": {
@@ -2341,6 +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"
+                  ]
+                }
+              }
             }
           ]
         }

diff --git a/workflows/downstream/downstream.wdl b/workflows/downstream/downstream.wdl
@@ -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
@@ -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
   }
 }