Added QCAssessment workflow to run stand-alone QC on ILMN samples. (Primarily for malaria work)

Author: jonn-smith

wdl/pipelines/ILMN/QualityControl/QCAssessment.wdl

@@ -0,0 +1,79 @@
+version 1.0
+
+import "../../../tasks/QC/QCAssessment.wdl" as QCAssessment
+import "../../../tasks/QC/FastQC.wdl" as FastQC
+import "../../../tasks/QC/AlignedMetrics.wdl" as AM
+
+workflow QCAssessment {
+    meta {
+        description: "Assess quality metrics from mosdepth coverage and callable loci data to determine pass/fail status.  To pass, the fraction of callable bases must be greater than min_callable_fraction and at least min_coverage_threshold_regions fraction of the genome must have a coverage depth greater than min_coverage."
+    }
+
+    parameter_meta {
+        bam: "Bam file to assess"
+        bai: "Index file for given bam file"
+        coverage_bed_file: "Bed file for regions to assess"
+        min_coverage: "Minimum required mean coverage depth (default: 5)"
+        min_coverage_threshold_regions: "Minimum required fraction of genome that must have a coverage depth greater than min_coverage (default: 0.2)"
+        min_callable_fraction: "Minimum required fraction of genome that is callable (default: 0.50)"
+        prefix: "Prefix for output files"
+    }
+
+    input {
+        File bam
+        File bai
+        File coverage_bed_file
+
+        String prefix
+
+        Float min_coverage = 5
+        Float min_coverage_threshold_regions = 0.2
+        Float min_callable_fraction = 0.50
+
+        RuntimeAttr? runtime_attr_override
+    }
+
+    call AM.MosDepthOverBed as t_001_MosDepthOverBed {
+            input:
+                bam = bam,
+                bai = bai,
+                bed = select_first(coverage_bed_file)
+        }
+
+    call QCAssessment.AssessQualityMetrics as t_002_AssessQualityMetrics {
+        input:
+            callable_loci_summary = t_001_MosDepthOverBed.callable_loci_summary,
+            mosdepth_region_bed = t_001_MosDepthOverBed.regions,
+            min_coverage = min_coverage,
+            min_coverage_threshold_regions = min_coverage_threshold_regions,
+            min_callable_fraction = min_callable_fraction,
+            prefix = SM
+    }
+
+    call FastQC.FastQC as t_003_FastQC { 
+        input: 
+            bam = bam, 
+            bai = bai 
+    }
+
+    output {
+ 
+        # Primary outputs:
+        String qc_status = t_002_AssessQualityMetrics.qc_status
+        String qc_message = t_002_AssessQualityMetrics.qc_message
+
+        # Mosdepth outputs:
+        File mosdepth_global_dist = t_001_MosDepthOverBed.global_dist
+        File mosdepth_region_dist = t_001_MosDepthOverBed.region_dist
+        File mosdepth_regions = t_001_MosDepthOverBed.regions
+        File mosdepth_regions_csi = t_001_MosDepthOverBed.regions_csi
+
+        # Callable loci outputs:
+        File callable_loci_summary = select_first([t_001_MosDepthOverBed.callable_loci_summary, t_002_AssessQualityMetrics.callable_loci_summary])
+        File callable_loci_bed = select_first([t_001_MosDepthOverBed.callable_loci_bed, t_002_AssessQualityMetrics.callable_loci_bed])
+
+        # FastQC outputs:
+        File fastqc_zip = t_003_FastQC.fastqc_zip
+        File fastqc_html = t_003_FastQC.fastqc_html
+    }
+}