modify outputPath category from required to common

bcftools.wdl

@@ -45,7 +45,7 @@ task Bcf2Vcf {
 
     parameter_meta {
         bcf: {description: "The generated BCF from an SV caller", category: "required"}
-        outputPath: {description: "The location the output VCF file should be written.", category: "required"}
+        outputPath: {description: "The location the output VCF file should be written.", category: "common"}
         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"}
     }
 }

clever.wdl

@@ -119,7 +119,7 @@ task Prediction {
         bamFile: {description: "The bam file to process.", category: "required"}
         bamIndex: {description: "The index bam file.", category: "required"}
         bwaIndex: {description: "The BWA index files.", category: "required"}
-        outputPath: {description: "The location the output VCF file should be written.", category: "required"}
+        outputPath: {description: "The location the output VCF file should be written.", category: "common"}
         threads: {description: "The the number of threads required to run a program", category: "advanced"}
         memory: {description: "The memory required to run the programs", category: "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"}

delly.wdl

@@ -58,7 +58,7 @@ task CallSV {
         bamIndex: {description: "The index bam file.", category: "required"}
         referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
         referenceFastaFai: {description: "Fasta index (.fai) file of the reference", category: "required" }
-        outputPath: {description: "The location the output VCF file should be written.", category: "required"}
+        outputPath: {description: "The location the output VCF file should be written.", category: "common"}
         memory: {description: "The memory required to run the programs", category: "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"}
     }

manta.wdl

@@ -68,7 +68,7 @@ task Germline {
         bamIndex: {description: "The index bam file.", category: "required"}
         referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
         referenceFastaFai: {description: "Fasta index (.fai) file of the reference", category: "required" }
-        runDir: {description: "The directory to use as run/output directory.", category: "required"}
+        runDir: {description: "The directory to use as run/output directory.", category: "common"}
         callRegions: {description: "The bed file which indicates the regions to operate on.", category: "common"}
         callRegionsIndex: {description: "The index of the bed file which indicates the regions to operate on.", category: "common"}
         exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}

picard.wdl

@@ -671,7 +671,7 @@ task RenameSample {
     parameter_meta {
         # inputs
         inputVcf: {description: "The VCF file to process.", category: "required"}
-        outputPath: {description: "The location the output VCF file should be written.", category: "required"}
+        outputPath: {description: "The location the output VCF file should be written.", category: "common"}
         newSampleName: {description: "A string to replace the old sample name.", category: "required"}
         memory: {description: "The memory required to run the programs", category: "advanced"}
         javaXmx: {description: "The max. memory allocated for JAVA", category: "advanced"}

samtools.wdl

@@ -425,7 +425,7 @@ task FilterShortReadsBam {
 
     parameter_meta {
         bamFile: {description: "The bam file to process.", category: "required"}
-        outputPathBam: {description: "The filtered bam file.", category: "required"}
+        outputPathBam: {description: "The filtered bam file.", category: "common"}
         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"}
     }
 }

survivor.wdl

@@ -69,7 +69,7 @@ task Merge {
         strandType: {description: "A boolean to include strand type of an SV to be merged", category: "advanced"}
         distanceBySvSize: {description: "A boolean to predict the pairwise distance between the SVs based on their size", category: "advanced"}
         minSize: {description: "The mimimum size of SV to be merged", category: "advanced"}
-        outputPath: {description: "The location the output VCF file should be written.", category: "required"}
+        outputPath: {description: "The location the output VCF file should be written.", category: "common"}
         memory: {description: "The memory required to run the programs", category: "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"}
     }