diff --git a/bcftools.wdl b/bcftools.wdl index 866a31016c7887c4d3cfe09bacb948a8d2d8eca8..122fcdd1e4ee0a5cc468b9b1f15d884813ac5058 100644 --- a/bcftools.wdl +++ b/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"} } } diff --git a/clever.wdl b/clever.wdl index ca28336ed80566fe3a629566a968c51cde4c2a6d..33ac26f232440368c25c60245a7e7925ea2f2084 100644 --- a/clever.wdl +++ b/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"} diff --git a/delly.wdl b/delly.wdl index fab0637156402bf9198068bd7913f8c1d0f7c348..ad8f18d9579d35ab161499cfd70cf28742fa1ce6 100644 --- a/delly.wdl +++ b/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"} } diff --git a/manta.wdl b/manta.wdl index cd869bb19bb518306071b78506ff6715fd41c919..5006a01efb5d92a97d527fa26b5866db959c3329 100644 --- a/manta.wdl +++ b/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"} diff --git a/picard.wdl b/picard.wdl index 88ea3a2e88e5fa8ee5eb6e2f4f44bbb1716790a7..7df96aa93e758566419a73f7a98f01669cb7d3d6 100644 --- a/picard.wdl +++ b/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"} diff --git a/samtools.wdl b/samtools.wdl index b04dd11774ba7e3414fca751f32f68b2374bc020..de7f2a3652e1940bb343ecf77abb528eec679d7c 100644 --- a/samtools.wdl +++ b/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"} } } diff --git a/survivor.wdl b/survivor.wdl index 15bff093aecab510b13a76ee3f7c92d398796666..ded11d75a64b9de98312a520d0fd284aa0ecda5c 100644 --- a/survivor.wdl +++ b/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"} }