diff --git a/CHANGELOG.md b/CHANGELOG.md index 2b8de510fd9c6721c9d6206c2fb434afc122c39b..7889194141e364c34d635ee653c96fee958c8f3c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,7 +19,10 @@ version 4.0.0-develop Perl wrapper for FastQC. This has the advantage that memory and threads can be set independently. A rather high maximum heap size of 1750MB (Xmx1750M) was set, as OOM errors occurred frequently on some fastqs. -+ Added bcftools stats task. ++ STAR: Add options regarding alignment score (regarding read length as well) + for tweaking when processing rRNA depleted samples. ++ TALON: Update `minimumIdentity` to correct type (float, was integer) + & set new default according to developers (0.8, was 0). + Added GATK VariantEval task. + Added a log output for STAR. + Added report output to Hisat2. diff --git a/common.wdl b/common.wdl index f83255230874d77350b2d662e643f5e5e1f75aa2..e96cc1c814fc7294a2b5c0da7befa5adcedd974c 100644 --- a/common.wdl +++ b/common.wdl @@ -243,7 +243,7 @@ task YamlToJson { parameter_meta { yaml: {description: "The YAML file to convert.", category: "required"} outputJson: {description: "The location the output JSON file should be written to.", category: "advanced"} - memory: {description: "The maximum aount of memroy the job will need.", category: "advanced"} + memory: {description: "The maximum amount of memory the job will need.", category: "advanced"} timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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/star.wdl b/star.wdl index bc47bc02377c757139c81a02755b1843210a4077..4c1341713d3729b6e362dad074bff1832bf390a4 100644 --- a/star.wdl +++ b/star.wdl @@ -95,6 +95,10 @@ task Star { String outFileNamePrefix String outSAMtype = "BAM SortedByCoordinate" String readFilesCommand = "zcat" + Int? outFilterScoreMin + Float? outFilterScoreMinOverLread + Int? outFilterMatchNmin + Float? outFilterMatchNminOverLread String? outStd String? twopassMode = "Basic" Array[String]? outSAMattrRGline @@ -124,6 +128,10 @@ task Star { --genomeDir ~{sub(indexFiles[0], basename(indexFiles[0]), "")} \ --outSAMtype ~{outSAMtype} \ --readFilesCommand ~{readFilesCommand} \ + ~{"--outFilterScoreMin " + outFilterScoreMin} \ + ~{"--outFilterScoreMinOverLread " + outFilterScoreMinOverLread} \ + ~{"--outFilterMatchNmin " + outFilterMatchNmin} \ + ~{"--outFilterMatchNminOverLread " + outFilterMatchNminOverLread} \ ~{"--outSAMunmapped " + outSAMunmapped} \ ~{"--runThreadN " + runThreadN} \ ~{"--outStd " + outStd} \ @@ -151,6 +159,10 @@ task Star { outFileNamePrefix: {description: "The prefix for the output files. May include directories.", category: "required"} outSAMtype: {description: "The type of alignment file to be produced. Currently only `BAM SortedByCoordinate` is supported.", category: "advanced"} readFilesCommand: {description: "Equivalent to star's `--readFilesCommand` option.", category: "advanced"} + outFilterScoreMin: {description: "Equivalent to star's `--outFilterScoreMin` option.", category: "advanced"} + outFilterScoreMinOverLread: {description: "Equivalent to star's `--outFilterScoreMinOverLread` option.", category: "advanced"} + outFilterMatchNmin: {description: "Equivalent to star's `--outFilterMatchNmin` option.", category: "advanced"} + outFilterMatchNminOverLread: {description: "Equivalent to star's `--outFilterMatchNminOverLread` option.", category: "advanced"} outStd: {description: "Equivalent to star's `--outStd` option.", category: "advanced"} twopassMode: {description: "Equivalent to star's `--twopassMode` option.", category: "advanced"} outSAMattrRGline: {description: "The readgroup lines for the fastq pairs given (in the same order as the fastq files).", category: "common"} @@ -159,8 +171,7 @@ task Star { runThreadN: {description: "The number of threads to use.", category: "advanced"} memory: {description: "The amount of memory this job will use.", category: "advanced"} timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"} + 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/talon.wdl b/talon.wdl index b2ae3a622067184bfb6fc5524cdd7b137460d10e..98e0c13a7af5ebe3029f02522dbcdcbbd35c905c 100644 --- a/talon.wdl +++ b/talon.wdl @@ -380,7 +380,7 @@ task Talon { File databaseFile String genomeBuild Float minimumCoverage = 0.9 - Int minimumIdentity = 0 + Float minimumIdentity = 0.8 String outputPrefix Int cores = 4