diff --git a/clever.wdl b/clever.wdl index 863bf7efb84a3731ab073a678f9d80607d503edc..e1b1777995c916b6a5f8c725a5cb7b98d3731e12 100644 --- a/clever.wdl +++ b/clever.wdl @@ -41,6 +41,8 @@ task Prediction { 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"} bwaIndex: {description: "The BWA index files.", category: "required"} + memory: {description: "The memory required to run the programs", category: "common"} + threads: {description: "The the number of threads required to run a program", category: "common"} } } @@ -94,5 +96,7 @@ task Mateclever { category: "advanced"} bwaIndex: {description: "The BWA index files.", category: "required"} predictions: {description: "The predicted deletions (VCF) from clever.", category: "required"} + memory: {description: "The memory required to run the programs", category: "common"} + threads: {description: "The the number of threads required to run a program", category: "common"} } } diff --git a/delly.wdl b/delly.wdl index baaef56c013c9a6c54aa2bd076dd132998c825ee..940b5d35d65ce1f7472768fe8bebc325ef7e7740 100644 --- a/delly.wdl +++ b/delly.wdl @@ -39,5 +39,6 @@ task CallSV { 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"} + memory: {description: "The memory required to run the programs", category: "common"} } } diff --git a/manta.wdl b/manta.wdl index d44ff0a4b97c26319c2847a0619f53a8dd86ac9c..9c79786cd427296c77c19c2a17ea4b0a6eaa24b2 100644 --- a/manta.wdl +++ b/manta.wdl @@ -128,6 +128,8 @@ task Germline { 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"} + memoryGb: {description: "The memory required to run the manta", category: "common"} + cores: {description: "The the number of cores required to run a program", category: "common"} } } diff --git a/picard.wdl b/picard.wdl index 5b3c3c65681e8a45ba4a900160af10cf688d0ea9..6f85bfd8e6b656f27c85b00309adea51c4d2ce75 100644 --- a/picard.wdl +++ b/picard.wdl @@ -647,6 +647,8 @@ task RenameSample { 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"} + javaXmx: {description: "The max. memory allocated for JAVA", category: "common"} + memory: {description: "The memory required to run the programs", category: "common"} } } diff --git a/survivor.wdl b/survivor.wdl index 8763053d4ef6da81d449bf0a804c19650144fd93..bf147816025851052941cb00d35ba259f51de473 100644 --- a/survivor.wdl +++ b/survivor.wdl @@ -47,5 +47,12 @@ task Merge { 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"} + minSize: {description: "The mimimum size of SV to be merged", category: "required"} + distanceBySvSize: {description: "A boolean to predict the pairwise distance between the SVs based on their size", category: "required"} + strandType: {description: "A boolean to include strand type of an SV to be merged", category: "required"} + svType: {description: "A boolean to include the type SV to be merged", category: "required"} + suppVecs: {description: "The minimum number of SV callers to support the merging", category: "required"} + breakpointDistance: {description: "The distance between pairwise breakpoints between SVs", category: "required"} + memory: {description: "The memory required to run the programs", category: "common"} } }