Support input without rq values.

PacificBiosciences · Dec 10, 2024 · 342d259 · 342d259
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commit 342d259
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Showing 7 changed files with 34 additions and 6 deletions.
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. |  |

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. |  |

diff --git a/wdl-ci.config.json b/wdl-ci.config.json
@@ -1382,6 +1382,34 @@
                   ]
                 }
               }
+            },
+            {
+              "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"
+                  ]
+                }
+              }
             }
           ]
         }

diff --git a/workflows/family.wdl b/workflows/family.wdl
@@ -273,7 +273,7 @@ workflow humanwgs_family {
     # 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?] 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

diff --git a/workflows/singleton.wdl b/workflows/singleton.wdl
@@ -213,7 +213,7 @@ workflow humanwgs_singleton {
     # bam stats
     File   bam_stats                = upstream.read_length_and_quality
     File   read_length_plot         = upstream.read_length_plot
-    File   read_quality_plot        = upstream.read_quality_plot
+    File?  read_quality_plot        = upstream.read_quality_plot
     String stat_num_reads           = upstream.stat_num_reads
     String stat_read_length_mean    = upstream.stat_read_length_mean
     String stat_read_length_median  = upstream.stat_read_length_median

diff --git a/workflows/upstream/upstream.wdl b/workflows/upstream/upstream.wdl
@@ -219,7 +219,7 @@ workflow upstream {
     # bam stats
     File   read_length_and_quality  = merge_bam_stats.read_length_and_quality
     File   read_length_plot         = merge_bam_stats.read_length_plot
-    File   read_quality_plot        = merge_bam_stats.read_quality_plot
+    File?  read_quality_plot        = merge_bam_stats.read_quality_plot
     String stat_num_reads           = merge_bam_stats.stat_num_reads
     String stat_read_length_mean    = merge_bam_stats.stat_read_length_mean
     String stat_read_length_median  = merge_bam_stats.stat_read_length_median

diff --git a/workflows/wdl-common b/workflows/wdl-common
+20 −24		wdl/tasks/merge_bam_stats.wdl
+8 −5		wdl/tasks/pbmm2.wdl