Edit another batch of tasks to uniform layout.

b131d926 · JasperBoom · f4fee79b · b131d926 · b131d926 · b131d926
Commit b131d926 authored 4 years ago by JasperBoom
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -37,18 +37,18 @@ task Bam2Fasta {

    command {
        set -e
-        mkdir -p "$(dirname ~{outputPrefix})"'
+        mkdir -p "$(dirname ~{outputPrefix})"

        # Localise the bam and pbi files so they are next to each other in the
        # current folder.
        bamFiles=""
-        for bamFile in ~{sep=" " bam};
+        for bamFile in ~{sep=" " bam}
        do
            ln ${bamFile} .
            bamFiles=${bamFiles}" $(basename ${bamFile})"
        done

-        for index in ~{sep=" " bamIndex};
+        for index in ~{sep=" " bamIndex}
        do
            ln ${index} .
        done
@@ -110,13 +110,13 @@ task Bam2Fastq {
        # Localise the bam and pbi files so they are next to each other in the
        # current folder.
        bamFiles=""
-        for bamFile in ~{sep=" " bam};
+        for bamFile in ~{sep=" " bam}
        do
            ln ${bamFile} .
            bamFiles=${bamFiles}" $(basename ${bamFile})"
        done

-        for index in ~{sep=" " bamIndex};
+        for index in ~{sep=" " bamIndex}
        do
            ln ${index} .
        done

--- a/delly.wdl
+++ b/delly.wdl
 version 1.0

-# MIT License
-#
 # Copyright (c) 2018 Leiden University Medical Center
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -59,9 +57,9 @@ task CallSV {
        bamFile: {description: "The bam file to process.", category: "required"}
        bamIndex: {description: "The index bam file.", category: "required"}
        referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
-        referenceFastaFai: {description: "Fasta index (.fai) file of the reference", category: "required" }
+        referenceFastaFai: {description: "Fasta index (.fai) file of the reference.", category: "required" }
        outputPath: {description: "The location the output VCF file should be written.", category: "common"}
-        memory: {description: "The memory required to run the programs", category: "advanced"}
+        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"}
    }

--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -29,6 +29,7 @@ task Fastqc {
        Boolean noFilter = false
        Boolean extract = false
        Boolean nogroup = false
+
        Int? minLength
        String? format
        File? contaminants
@@ -37,32 +38,35 @@ task Fastqc {
        Int? kmers
        String? dir

-        Int threads = 1
        # Set javaXmx a little high. Equal to fastqc default with 7 threads.
        # This is because some fastq files need more memory. 2G per core
        # is a nice cluster default, so we use all the rest of the memory for
        # fastqc so we should have as little OOM crashes as possible even with
        # weird edge case fastq's.
-        String javaXmx="1750M"  
+        String javaXmx="1750M"
+        Int threads = 1
        String memory = "2G"
        Int timeMinutes = 1 + ceil(size(seqFile, "G")) * 4
-        String dockerImage = "quay.io/biocontainers/fastqc:0.11.9--0"
-        Array[File]? NoneArray
-        File? NoneFile
+        String dockerImage = "quay.io/biocontainers/fastqc:0.11.9--0
+
+        Array[File]? noneArray
+        File? noneFile
    }

    # Chops of the .gz extension if present.
-    # The Basename needs to be taken here. Otherwise paths might differ between similar jobs.
+    # The Basename needs to be taken here. Otherwise paths might differ
+    # between similar jobs.
    String name = basename(sub(seqFile, "\.gz$",""))
-    # This regex chops of the extension and replaces it with _fastqc for the reportdir.
+    # This regex chops of the extension and replaces it with _fastqc for
+    # the reportdir.
    # Just as fastqc does it.
    String reportDir = outdirPath + "/" + sub(name, "\.[^\.]*$", "_fastqc")

-    # We reimplement the perl wrapper here. This has the advantage that it gives
-    # us more control over the amount of memory used.
+    # We reimplement the perl wrapper here. This has the advantage that it
+    # gives us more control over the amount of memory used.
    command <<<
        set -e
-        mkdir -p ~{outdirPath}
+        mkdir -p "~{outdirPath}"
        FASTQC_DIR="/usr/local/opt/fastqc-0.11.9"
        export CLASSPATH="$FASTQC_DIR:$FASTQC_DIR/sam-1.103.jar:$FASTQC_DIR/jbzip2-0.9.jar:$FASTQC_DIR/cisd-jhdf5.jar"
        java -Djava.awt.headless=true -XX:ParallelGCThreads=1 \
@@ -86,23 +90,24 @@ task Fastqc {
    >>>

    output {
-        File? rawReport = if extract then reportDir + "/fastqc_data.txt" else NoneFile
        File htmlReport = reportDir + ".html"
        File reportZip = reportDir + ".zip"
-        File? summary = if extract then reportDir + "/summary.txt" else NoneFile
-        Array[File]? images = if extract then glob(reportDir + "/Images/*.png") else NoneArray
+        File? summary = if extract then reportDir + "/summary.txt" else noneFile
+        File? rawReport = if extract then reportDir + "/fastqc_data.txt" else noneFile
+        Array[File]? images = if extract then glob(reportDir + "/Images/*.png") else noneArray
    }

    runtime {
        cpu: threads
        memory: memory
-        docker: dockerImage
        time_minutes: timeMinutes
+        docker: dockerImage
    }

    parameter_meta {
+        # inputs
        seqFile: {description: "A fastq file.", category: "required"}
-        outdirPath: {description: "The path to write the output to", catgory: "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"}
@@ -115,18 +120,16 @@ task Fastqc {
        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"}
+        javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
        threads: {description: "The number of cores to use.", category: "advanced"}
-        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"}
+        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"]
+            exclude: ["noneFile", "noneArray"]
        }
    }
 }
@@ -155,14 +158,14 @@ task GetConfiguration {
    }

    runtime {
-        memory: "2G" # Needs more than 1 to pull the docker image
+        memory: "2G" # Needs more than 1 to pull the docker image.
        time_minute: timeMinutes
        docker: dockerImage
    }

    parameter_meta {
+        # inputs
        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"}
    }
 }
--- a/fastqsplitter.wdl
+++ b/fastqsplitter.wdl
 version 1.0

-# MIT License
-#
 # Copyright (c) 2019 Leiden University Medical Center
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -26,19 +24,24 @@ task Fastqsplitter {
    input {
        File inputFastq
        Array[String]+ outputPaths
-        String dockerImage = "quay.io/biocontainers/fastqsplitter:1.1.0--py37h516909a_1"
+
        Int? compressionLevel
        Int? threadsPerFile
-         # fastqplitter utilizes one thread per input file and one or more threads per output file + one thread for the application.
-         # Since a compression level of 1 is used, each output file uses approx 0.5 cores.
+
+        # fastqplitter utilizes one thread per input file and one or
+        # more threads per output file + one thread for the application.
+        # Since a compression level of 1 is used, each output file
+        # uses approx 0.5 cores.
        Int cores = 1 + ceil(0.5 * length(outputPaths))
+        String dockerImage = "quay.io/biocontainers/fastqsplitter:1.1.0--py37h516909a_1"
    }

    # Busybox mkdir does not accept multiple paths.
    command <<<
        set -e
        for FILE in ~{sep=' ' outputPaths}
-            do mkdir -p "$(dirname $FILE)"
+        do
+            mkdir -p "$(dirname ${FILE})"
        done
        fastqsplitter \
        ~{"-c " + compressionLevel} \
@@ -51,15 +54,16 @@ task Fastqsplitter {
        Array[File] chunks = outputPaths
    }

-    # Using very safe margins here. 10MB/300MB per outputfile is used for single-threaded/multi-threaded compression.
+    # Using very safe margins here. 10MB/300MB per outputfile is used for
+    # single-threaded/multi-threaded compression.
    Float memoryPerFile = if select_first([threadsPerFile, 1]) > 1 then 0.40 else 0.02
    Int fastqsplitterMemory = ceil(0.100 + memoryPerFile * length(outputPaths))
-    # Make sure a minimum of 2 GB is present to pull the singularity image
+    # Make sure a minimum of 2 GB is present to pull the singularity image.
    Int memory = if fastqsplitterMemory <= 2 then 2 else fastqsplitterMemory

    runtime {
+        cpu: cores
        memory: "~{memory}G"
        docker: dockerImage
-        cpu: cores
    }
 }
--- a/flash.wdl
+++ b/flash.wdl
@@ -24,13 +24,14 @@ import "common.wdl" as common

 task Flash {
    input {
-        String? preCommand
        FastqPair inputFastq
        String outdirPath
        String outPrefix = "flash"
+        Boolean compress = true
+
+        String? preCommand
        Int? minOverlap
        Int? maxOverlap
-        Boolean compress = true

        Int threads = 2
        String memory = "2G"
@@ -55,8 +56,8 @@ task Flash {
        File notCombined1 = outdirPath + "/" + outPrefix + ".notCombined_1.fastq.gz"
        File notCombined2 = outdirPath + "/" + outPrefix + ".notCombined_2.fastq.gz"
        FastqPair notCombined = object {
-          R1: notCombined1,
-          R2: notCombined2
+            R1: notCombined1,
+            R2: notCombined2
        }
        File hist = outdirPath + "/" + outPrefix + ".hist"
        File histogram = outdirPath + "/" + outPrefix + ".histogram"
@@ -66,5 +67,4 @@ task Flash {
        cpu: threads
        memory: memory
    }
-
-}
\ No newline at end of file
+}
--- a/gatk.wdl
+++ b/gatk.wdl
--- a/gffcompare.wdl
+++ b/gffcompare.wdl
@@ -147,4 +147,4 @@ task GffCompare {
            exclude: ["noneFile"]
        }
    }
-}
\ No newline at end of file
+}