diff --git a/bwa.wdl b/bwa.wdl index f821b9173ed1a6f64aaf854a0e885f4822dca617..6623899134615340dffd9d2def09e3e4379c9b88 100644 --- a/bwa.wdl +++ b/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" } diff --git a/collect-columns.wdl b/collect-columns.wdl index 8ed72320ed437a737366d6cdae0148a200484050..914c785f25a186e9c868bd5dccc8dfed5ad57fab 100644 --- a/collect-columns.wdl +++ b/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" } } diff --git a/cutadapt.wdl b/cutadapt.wdl index f663071b0012a0dfaeab53f3c3e6db871a35417e..9c869c2a416dff02d9025d8d8944d2e2409dca89 100644 --- a/cutadapt.wdl +++ b/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" } } diff --git a/fastqc.wdl b/fastqc.wdl index 4c68cd26b13f4af531e84dc4de2851b3da76bd96..a50a1c2826998c8e42505d097d7a94dedee68f3d 100644 --- a/fastqc.wdl +++ b/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" + } + } } diff --git a/htseq.wdl b/htseq.wdl index ad83ac35aec21c0b321377317277158af0df68be..645396e8061179df2d119d61baef6cac35af1b59 100644 --- a/htseq.wdl +++ b/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" } } diff --git a/stringtie.wdl b/stringtie.wdl index f02629874c5d10c7d4ad2170dc11b2cb06923905..b9bfade39a219e3ac5c933e252b41aafd55ef0d7 100644 --- a/stringtie.wdl +++ b/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" } }