add parameter_meta to fastqc

bwa.wdl

@@ -104,7 +104,7 @@ task Kit {
             category: "required"
         }
         outputPrefix: {
-            description: "The prefix of the output files, including any parent directories",
+            description: "The prefix of the output files, including any parent directories.",
             category: "required"
         }
         readgroup: {
@@ -128,7 +128,7 @@ task Kit {
             category: "advanced"
         }
         dockerImage: {
-            description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+            description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
             category: "advanced"
         }
 

collect-columns.wdl

@@ -85,7 +85,7 @@ task CollectColumns {
             category: "advanced"
         }
         dockerImage: {
-            description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+            description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
             category: "advanced"
         }
     }

cutadapt.wdl

@@ -374,7 +374,7 @@ task Cutadapt {
             catgeory: "advanced"
         }
         cores: {
-            description: "The number of cores to use",
+            description: "The number of cores to use.",
             catgeory: "advanced"
         }
         memory: {
@@ -382,7 +382,7 @@ task Cutadapt {
             category: "advanced"
         }
         dockerImage: {
-            description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+            description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
             category: "advanced"
         }
     }

fastqc.wdl

@@ -63,6 +63,79 @@ task Fastqc {
         cpu: threads
         docker: dockerImage
     }
+
+    parameter_meta {
+        seqFile: {
+            description: "A FastQ file.",
+            category: "required"
+        }
+        outdirPath: {
+            description: "The path to write the output to",
+            catgory: "required"
+        }
+        casava: {
+            description: "Equivalent to fastqc's --casava flag.",
+            catgeory: "advanced"
+        }
+        nano: {
+            description: "Equivalent to fastqc's --nano flag.",
+            catgeory: "advanced"
+        }
+        noFilter: {
+            description: "Equivalent to fastqc's --nofilter flag.",
+            catgeory: "advanced"
+        }
+        extract: {
+            description: "Equivalent to fastqc's --extract flag.",
+            catgeory: "advanced"
+        }
+        nogroup: {
+            description: "Equivalent to fastqc's --nogroup flag.",
+            catgeory: "advanced"
+        }
+        minLength: {
+            description: "Equivalent to fastqc's --min_length option.",
+            catgeory: "advanced"
+        }
+        format: {
+            description: "Equivalent to fastqc's --format option.",
+            catgeory: "advanced"
+        }
+        contaminants: {
+            description: "Equivalent to fastqc's --contaminants option.",
+            catgeory: "advanced"
+        }
+        adapters: {
+            description: "Equivalent to fastqc's --adapters option.",
+            catgeory: "advanced"
+        }
+        limits: {
+            description: "Equivalent to fastqc's --limits option.",
+            catgeory: "advanced"
+        }
+        kmers: {
+            description: "Equivalent to fastqc's --kmers option.",
+            catgeory: "advanced"
+        }
+        dir: {
+            description: "Equivalent to fastqc's --dir option.",
+            catgeory: "advanced"
+        }
+        threads: {
+            description: "The number of cores to use.",
+            catgeory: "advanced"
+        }
+        dockerImage: {
+            description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+            category: "advanced"
+        }
+    }
+
+    meta {
+        WDL_AID: {
+            exclude: ["NoneFile", "NoneArray"]
+        }
+    }
 }
 
 task GetConfiguration {
@@ -89,4 +162,11 @@ task GetConfiguration {
         memory: "2G" # Needs more than 1 to pull the docker image
         docker: dockerImage
     }
+
+    parameter_meta {
+        dockerImage: {
+            description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+            category: "advanced"
+        }
+    }
 }

htseq.wdl

@@ -82,7 +82,7 @@ task HTSeqCount {
             category: "advanced"
         }
         dockerImage: {
-            description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+            description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
             category: "advanced"
         }
     }

stringtie.wdl

@@ -83,7 +83,7 @@ task Stringtie {
             category: "advanced"
         }
         dockerImage: {
-            description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+            description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
             category: "advanced"
         }
     }
@@ -177,7 +177,7 @@ task Merge {
             category: "advanced"
         }
         dockerImage: {
-            description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+            description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
             category: "advanced"
         }
     }