Update picard.

7dab07f8 · JasperBoom · 7d76ed6c · 7dab07f8 · 7dab07f8
Commit 7dab07f8 authored 4 years ago by JasperBoom
--- a/TO-DO.md
+++ b/TO-DO.md
@@ -23,6 +23,7 @@ Some tasks are importing other WDL files.
 * spades.wdl: `Spades`
 * unicycler.wdl: `Unicycler`
 * wisestork.wdl: `Count`, `GcCorrect`, `Newref`, `Zscore`
+* picard.wdl: `ScatterIntervalList`

 ## Imports other tasks:
 * bamstats.wdl

--- a/picard.wdl
+++ b/picard.wdl
@@ -321,8 +321,8 @@ task CollectRnaSeqMetrics {
        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"}

        # outputs
-        metrics: {description: ""}
-        chart: {description: ""}
+        metrics: {description: "Metrics describing the distribution of bases within the transcripts."}
+        chart: {description: "Plot of normalized position vs. coverage."}
    }
 }

@@ -385,9 +385,9 @@ task CollectTargetedPcrMetrics {
        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"}

        # outputs
-        perTargetCoverage: {description: ""}
-        perBaseCoverage: {description: ""}
-        metrics: {description: ""}
+        perTargetCoverage: {description: "Per target coverage information."}
+        perBaseCoverage: {description: "Per base coverage information to."}
+        metrics: {description: "File containing metrics."}
    }
 }

@@ -539,6 +539,11 @@ task GatherBamFiles {
        memoryMb: {description: "The amount of memory this job will use in megabytes.", 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"}
+
+        # outputs
+        outputBam: {description: ""}
+        outputBamIndex: {description: ""}
+        outputBamMd5: {description: ""}
    }
 }

@@ -582,6 +587,9 @@ task GatherVcfs {
        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"}
+
+        # outputs
+        outputVcf: {description: ""}
    }
 }

@@ -666,6 +674,12 @@ task MarkDuplicates {
        memoryMb: {description: "The amount of memory this job will use in megabytes.", 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"}
+
+        # outputs
+        outputBam: {description: ""}
+        outputBamIndex: {description: ""}
+        outputBamMd5: {description: ""}
+        metricsFile: {description: ""}
    }
 }

@@ -725,6 +739,10 @@ task MergeVCFs {
        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"}
+
+        # outputs
+        outputVcf: {description: "Multiple variant files combined into a single variant file."}
+        outputVcfIndex: {description: "Index of `outputVcf`."}
    }
 }

@@ -768,6 +786,21 @@ task SamToFastq {
        docker: dockerImage
    }

+    parameter_meta {
+        # inputs
+        inputBam: {description: "Input BAM file to extract reads from.", category: "required"}
+        inputBamIndex: {description: "Input BAM index file.", category: "required"}
+        paired: {description: "Set to false when input data is single-end.", category: "common"}
+        javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
+
+        # outputs
+        read1: {description: "Fastq file containing reads from the first pair."}
+        read2: {description: "Fastq file containing reads from the second pair."}
+        unpairedRead: {description: "Fastq file containing unpaired reads."}
+
    meta {
        WDL_AID: {
            exclude: ["noneFile"]
@@ -864,6 +897,10 @@ task SortSam {
        XmxGb: {description: "The maximum memory available to picard SortSam. Should be lower than `memory` to accommodate JVM overhead and BWA mem's memory usage.", 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"}
+
+        # outputs
+        outputBam: {description: "Sorted BAM file."}
+        outputBamIndex: {description: "Index of sorted BAM file."}
    }
 }

@@ -911,6 +948,10 @@ task SortVcf {
        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"}
+
+        # outputs
+        outputVcf: {description: "Sorted VCF file(s)."}
+        outputVcfIndex: {description: "Index(es) of sort(ed) VCF file(s)."}
    }
 }

@@ -955,5 +996,8 @@ task RenameSample {
        memory: {description: "The memory required to run the programs.", 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"}
+
+        # outputs
+        renamedVcf: {description: "New VCF with renamed sample."}
    }
 }