add multiqc task

multiqc.wdl

@@ -3,6 +3,7 @@ version 1.0
 task MultiQC {
     input {
         String? preCommand
+        File analysisDirectory
         Boolean force = false
         Boolean dirs = false
         Int? dirsDepth
@@ -16,9 +17,10 @@ task MultiQC {
         String? ignore
         String? ignoreSamples
         Boolean ignoreSymlinks = false
+        File? sampleNames
         File? fileList
-        Array[String] exclude
-        Array[String] module
+        Array[String]+? exclude
+        Array[String]+? module
         Boolean dataDir = false
         Boolean noDataDir = false
         String? dataFormat
@@ -28,12 +30,13 @@ task MultiQC {
         Boolean interactive = false
         Boolean lint = false
         Boolean pdf = false
-        Boolean noMegaQCUpload = true
+        Boolean megaQCUpload = false # This must be actively enabled in my opinion. The tools default is to upload.
         File? config  # A directory
         String? clConfig
         Boolean verbose  = false
         Boolean quiet = false
     }
+
     command {
         set -e -o pipefail
         ~{preCommand}
@@ -42,10 +45,33 @@ task MultiQC {
         ~{true="--dirs" false="" dirs} \
         ~{"--dirs-depth " + dirsDepth} \
         ~{true="--fullnames" false="" fullNames} \
-        ~{"--title " + title } \
-        ~{"--comment " + comment } \
+        ~{"--title " + title} \
+        ~{"--comment " + comment} \
         ~{"--filename " + fileName} \
-        ~{
+        ~{"--outdir " + outDir} \
+        ~{"--template " + template} \
+        ~{"--tag " + tag} \
+        ~{"--ignore " + ignore} \
+        ~{"--ignore-samples" + ignoreSamples} \
+        ~{true="--ignore-symlinks" false="" ignoreSymlinks} \
+        ~{"--sample-names " + sampleNames} \
+        ~{"--file-list " + fileList} \
+        ~{true="--exclude " false="" defined(exclude)}~{sep=" --exclude " select_first([exclude])} \
+        ~{true="--module " false="" defined(module)}~{sep=" --module " select_first([module])} \
+        ~{true="--data-dir" false="" dataDir} \
+        ~{true="--no-data-dir" false="" noDataDir} \
+        ~{"--data-format " + dataFormat} \
+        ~{true="--zip-data-dir" false="" zipDataDir} \
+        ~{true="--export" false="" export} \
+        ~{true="--flat" false="" flat} \
+        ~{true="--interactive" false="" interactive} \
+        ~{true="--lint" false="" lint} \
+        ~{true="--pdf" false="" pdf} \
+        ~{false="--no-megaqc-upload" true="" megaQCUpload} \
+        ~{"--config " + config} \
+        ~{"--cl-config " + clConfig } \
+        ~{analysisDirectory}
     }
+
     output {}
 }
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