updates based on PR suggestions

broadinstitute · Jul 16, 2024 · 4678f3a · 4678f3a
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diff --git a/CoverageProfiler/CoverageProfiler.wdl b/CoverageProfiler/CoverageProfiler.wdl
@@ -58,10 +58,7 @@ workflow coverageProfile {
         Float? DepthOfCoverageMeanCoverage = DepthOfCoverage.mean_coverage
         File? SamtoolsDepthProfile = SamtoolsDepth.depth_profile
         File? SamtoolsCovProfilePlot = CovProfileViz.cov_profile_plot
-        Float? SamtoolsAvgChrCovStd = CovProfileViz.avg_chr_cov_std
-        File? SamtoolsAvgChrCovPerChr = CovProfileViz.avg_chr_cov_per_chr
         Float? SamtoolsAvgCovMean = CovProfileViz.avg_cov_mean
-        File? SamtoolsAvgChrCovPerChrPlot = CovProfileViz.avg_chr_cov_per_chr_plot
     }
     meta {
         author: "Yueyao Gao"
@@ -150,7 +147,9 @@ workflow coverageProfile {
             Int? mem_gb
             Int? cpu
             Int? disk_size_gb
-            String samtools_docker = "euformatics/samtools:1.20"
+            Int preemptible = 1
+            Int maxRetries = 3
+            String samtools_docker = "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
     }
     command <<<
         # Create directories for input & output
@@ -177,8 +176,8 @@ workflow coverageProfile {
         cpu: select_first([cpu, 1])
         docker: samtools_docker
         disks: "local-disk ~{disk_size_gb} SSD"
-        preemptible: 0
-        maxRetries: 3
+        preemptible: preemptible
+        maxRetries: maxRetries
     }
 }
     task CovProfileViz {
@@ -189,7 +188,8 @@ workflow coverageProfile {
             String CovProfileViz_docker = "us-central1-docker.pkg.dev/tag-team-160914/gptag-dockers/covprofileviz:0.0.0"
             Int mem_gb = 32
             Int? cpu
-            Int? preemptible = 3
+            Int? preemptible = 1
+            Int MaxRetries = 3
             Int? disk_size_gb = 500
         }
         command <<<
@@ -205,16 +205,10 @@ workflow coverageProfile {
             -o output
 
             mv output/*_samtools_cov_with_gc.png output/~{sampleName}Sample_Cov_profile.png
-            mv output/*_avg_cov_per_chr.png output/~{sampleName}Avg_Cov_per_chr.png
-            mv output/*_avg_cov_std.txt output/~{sampleName}_Per_Chr_Cov_std.txt
-            mv output/*_avg_cov_per_chr.csv output/~{sampleName}_Per_Chr_Avg_cov.csv
             mv output/*_avg_cov_mean.txt output/~{sampleName}_Avg_Cov_mean.txt
         >>>
         output {
             File cov_profile_plot = "output/~{sampleName}Sample_Cov_profile.png"
-            File avg_chr_cov_per_chr_plot = "output/~{sampleName}Avg_Cov_per_chr.png"
-            Float avg_chr_cov_std = read_float("output/~{sampleName}_Per_Chr_Cov_std.txt")
-            File avg_chr_cov_per_chr = "output/~{sampleName}_Per_Chr_Avg_cov.csv"
             Float avg_cov_mean = read_float("output/~{sampleName}_Avg_Cov_mean.txt")
         }
         runtime {
@@ -223,6 +217,6 @@ workflow coverageProfile {
             docker: CovProfileViz_docker
             disks: "local-disk ~{disk_size_gb} SSD"
             preemptible: preemptible
-            maxRetries: 3
+            maxRetries: MaxRetries
         }
     }
diff --git a/CoverageProfiler/README.md b/CoverageProfiler/README.md
@@ -0,0 +1,93 @@
+# CoverageProfile WDL Workflow
+
+## Overview
+
+The `coverageProfile` workflow calculates the depth of coverage of an input sample and visualizes it. It supports two tools for depth calculation: Samtools and DepthOfCoverage (GATK). Visualization is available for Samtools and Exome data.
+
+## Inputs
+
+- `String sampleName` - The name of the sample.
+- `String coverageTool` - The tool to use for coverage calculation. Default is "Samtools".
+- `File alignedBam` - BAM file with aligned reads.
+- `File alignedBamIndex` - Index file for the BAM.
+- `File referenceFasta` - Reference genome in FASTA format.
+- `File referenceDict` - Dictionary file for the reference genome.
+- `File referenceFai` - Index file for the reference genome.
+- `File intervals` - Intervals file.
+- `File? interval_GCcontent_track` - (Optional) GC content track for visualization.
+- `Int MinBaseQuality` - Minimum base quality for coverage calculation. Default is 20.
+- `Int MinMappingQuality` - Minimum mapping quality for coverage calculation. Default is 20.
+- `Boolean visualise_coverage` - Whether to visualize the coverage. Default is false.
+
+## Outputs
+
+- `File? DepthOfCoverageIntervalCov` - Depth of coverage interval summary (only for DepthOfCoverage tool).
+- `Float? DepthOfCoverageMeanCoverage` - Mean coverage from DepthOfCoverage tool.
+- `File? SamtoolsDepthProfile` - Depth profile generated by Samtools.
+- `File? SamtoolsCovProfilePlot` - Coverage profile plot generated by visualization task.
+- `Float? SamtoolsAvgCovMean` - Average coverage mean from Samtools Depth.
+
+
+## Workflow
+
+### Main Workflow
+
+1. **Choose Tool:** Based on the `coverageTool` input, the workflow branches to use either Samtools or DepthOfCoverage.
+
+2. **Samtools Workflow:**
+   - Convert intervals to BED format using `IntervalListToBed`.
+   - Calculate depth using `SamtoolsDepth`.
+   - If `visualise_coverage` is true, visualize the coverage using `CovProfileViz`. The visualization requires the depth profile and a GC content track. It's currently only work with exome data. 
+
+3. **DepthOfCoverage Workflow:**
+   - Calculate depth using `DepthOfCoverage`.
+
+### Tasks
+
+#### DepthOfCoverage
+
+Calculates the depth of coverage using GATK's DepthOfCoverage tool.
+
+**Inputs:**
+- Various inputs for the BAM file, reference genome, intervals, and quality thresholds.
+
+**Outputs:**
+- `File sample_interval_summary` - Interval summary.
+- `Float mean_coverage` - Mean coverage.
+
+#### IntervalListToBed
+
+Converts an interval list to a BED file.
+
+**Inputs:**
+- `File intervals` - Intervals file.
+
+**Outputs:**
+- `File bed_intervals` - Converted BED file.
+
+#### SamtoolsDepth
+
+Calculates depth of coverage using Samtools.
+
+**Inputs:**
+- Various inputs for the BAM file, intervals, and quality thresholds.
+
+**Outputs:**
+- `File depth_profile` - Depth profile.
+
+#### CovProfileViz
+
+Visualizes the coverage profile.
+
+**Inputs:**
+- `File SamtoolsDepthProfile` - Depth profile from Samtools.
+- `File? GCcontentTrack` - Optional GC content track.
+- Other parameters for customization.
+
+**Outputs:**
+- `File cov_profile_plot` - Coverage profile plot.
+- `File avg_chr_cov_per_chr_plot` - Plot of average coverage per chromosome.
+- `Float avg_chr_cov_std` - Standard deviation of average coverage per chromosome.
+- `File avg_chr_cov_per_chr` - Average coverage per chromosome.
+- `Float avg_cov_mean` - Mean average coverage.
+