diff --git a/CHANGELOG.md b/CHANGELOG.md index 3f5a5d28a82cbb82e5e344dadabd6bdbedf75622..bac09da63d5fd848d8443ed98680a898cfb80042 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ that users understand how the changes affect the new version. version 2.2.0-dev --------------------------- ++ Add `memory` input to fastqc task. + Centrifuge: Fix issue where centrifuge would fail on incorrect paths. + Added GATK CNV calling tasks: + AnnotateIntervals diff --git a/fastqc.wdl b/fastqc.wdl index 1e835c4e9ac382b96ca1b6b5d9ce1cbce1e24dbd..31c2b80da54adebcd2acade8c8c634f4f0340ecc 100644 --- a/fastqc.wdl +++ b/fastqc.wdl @@ -18,6 +18,7 @@ task Fastqc { String? dir Int threads = 1 + String memory = "4G" String dockerImage = "quay.io/biocontainers/fastqc:0.11.7--4" Array[File]? NoneArray File? NoneFile @@ -61,74 +62,29 @@ task Fastqc { runtime { cpu: threads + memory: memory 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.", - category: "advanced" - } - nano: { - description: "Equivalent to fastqc's --nano flag.", - category: "advanced" - } - noFilter: { - description: "Equivalent to fastqc's --nofilter flag.", - category: "advanced" - } - extract: { - description: "Equivalent to fastqc's --extract flag.", - category: "advanced" - } - nogroup: { - description: "Equivalent to fastqc's --nogroup flag.", - category: "advanced" - } - minLength: { - description: "Equivalent to fastqc's --min_length option.", - category: "advanced" - } - format: { - description: "Equivalent to fastqc's --format option.", - category: "advanced" - } - contaminants: { - description: "Equivalent to fastqc's --contaminants option.", - category: "advanced" - } - adapters: { - description: "Equivalent to fastqc's --adapters option.", - category: "advanced" - } - limits: { - description: "Equivalent to fastqc's --limits option.", - category: "advanced" - } - kmers: { - description: "Equivalent to fastqc's --kmers option.", - category: "advanced" - } - dir: { - description: "Equivalent to fastqc's --dir option.", - category: "advanced" - } - threads: { - description: "The number of cores to use.", - 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" - } + 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.", category: "advanced"} + nano: {description: "Equivalent to fastqc's --nano flag.", category: "advanced"} + noFilter: {description: "Equivalent to fastqc's --nofilter flag.", category: "advanced"} + extract: {description: "Equivalent to fastqc's --extract flag.", category: "advanced"} + nogroup: {description: "Equivalent to fastqc's --nogroup flag.", category: "advanced"} + minLength: {description: "Equivalent to fastqc's --min_length option.", category: "advanced"} + format: {description: "Equivalent to fastqc's --format option.", category: "advanced"} + contaminants: {description: "Equivalent to fastqc's --contaminants option.", category: "advanced"} + adapters: {description: "Equivalent to fastqc's --adapters option.", category: "advanced"} + limits: {description: "Equivalent to fastqc's --limits option.", category: "advanced"} + kmers: {description: "Equivalent to fastqc's --kmers option.", category: "advanced"} + dir: {description: "Equivalent to fastqc's --dir option.", category: "advanced"} + threads: {description: "The number of cores to use.", category: "advanced"} + memory: {description: "The amount of memory this job will use.", 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"} } meta {