Fix input type bug

broadinstitute · Jun 17, 2024 · 0fc10bb · 0fc10bb
1 parent 46c7934
commit 0fc10bb
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Showing 2 changed files with 17 additions and 3 deletions.
diff --git a/CoverageProfiler/CoverageProfiler.inputs.json b/CoverageProfiler/CoverageProfiler.inputs.json
@@ -1,11 +1,22 @@
 {
   "coverageProfile.referenceFasta": "File",
+  "coverageProfile.SamtoolsDepth.samtools_docker": "String (optional, default = \"euformatics/samtools:1.20\")",
+  "coverageProfile.CovProfileViz.cpu": "Int? (optional)",
   "coverageProfile.DepthOfCoverage.gatk_docker": "String (optional, default = \"broadinstitute/gatk:4.5.0.0\")",
+  "coverageProfile.referenceDict": "File",
   "coverageProfile.intervals": "File",
+  "coverageProfile.referenceFai": "File",
   "coverageProfile.alignedBam": "File",
-  "coverageProfile.DepthOfCoverage.command_mem_mb": "Int? (optional)",
+  "coverageProfile.alignedBamIndex": "File",
+  "coverageProfile.coverageTool": "String (optional, default = \"Samtools\")",
   "coverageProfile.DepthOfCoverage.cpu": "Int? (optional)",
-  "coverageProfile.DepthOfCoverage.machine_mem_mb": "Int? (optional)",
+  "coverageProfile.SamtoolsDepth.cpu": "Int? (optional)",
+  "coverageProfile.MinMappingQuality": "Int (optional, default = 20)",
+  "coverageProfile.CovProfileViz.mem_gb": "Int? (optional)",
+  "coverageProfile.MinBaseQuality": "Int (optional, default = 20)",
+  "coverageProfile.CovProfileViz.CovProfileViz_docker": "String (optional, default = \"us-central1-docker.pkg.dev/tag-team-160914/gptag-dockers/covprofileviz:0.0.0\")",
+  "coverageProfile.SamtoolsDepth.mem_gb": "Int? (optional)",
+  "coverageProfile.interval_GCcontent_track": "File",
   "coverageProfile.DepthOfCoverage.mem_gb": "Int? (optional)",
   "coverageProfile.sampleName": "String"
 }

diff --git a/CoverageProfiler/CoverageProfiler.wdl b/CoverageProfiler/CoverageProfiler.wdl
@@ -53,6 +53,9 @@ workflow coverageProfile {
         File? DepthOfCoverageIntervalCov = DepthOfCoverage.sample_interval_summary
         Float? DepthOfCoverageMeanCoverage = DepthOfCoverage.mean_coverage
         File? SamtoolsDepthProfile = SamtoolsDepth.depth_profile
+        File? CovProfilePlot = CovProfileViz.cov_profile_plot
+        Float? AvgChrCovStd = CovProfileViz.avg_chr_cov_std
+        File? AvgChrCovPerChr = CovProfileViz.avg_chr_cov_per_chr
     }
     meta {
         author: "Yueyao Gao"
@@ -175,7 +178,7 @@ workflow coverageProfile {
             File GCcontentTrack
             String sampleName
             String CovProfileViz_docker = "us-central1-docker.pkg.dev/tag-team-160914/gptag-dockers/covprofileviz:0.0.0"
-            String? mem_gb
+            Int? mem_gb
             Int? cpu
         }
         command <<<