Merge branch 'develop' into biowdl-595

CHANGELOG.md

@@ -10,6 +10,9 @@ that users understand how the changes affect the new version.
 version 5.1.0-dev
 ---------------------------
 + Updated SURVIVOR version to 1.0.7
++ Add a combined samtools dict and samtools faidx task.
++ Add a BWA index task.
+
 + Move all memory notation to `KiB`, `MiB` and `GiB` from `K`, `M` and `G` 
   previously. The WDL spec clearly distuingishes between SI and binary 
   notations. Since Java always takes `K`, `M` and `G` to mean `KiB`, `MiB` and 

bwa.wdl

@@ -114,3 +114,48 @@ struct BwaIndex {
     File fastaFile
     Array[File] indexFiles
 }
+
+task Index {
+    input {
+        File fasta
+        String dockerImage = "quay.io/biocontainers/bwa:0.7.17--hed695b0_7"
+        Int? timeMinutes = 5 + ceil(size(fasta, "G") * 5)
+    }
+    String indexedFile = basename(fasta)
+
+    command {
+        set -e
+        cp ~{fasta} ~{indexedFile}
+        bwa index ~{indexedFile}
+    }
+
+    output {
+        BwaIndex index = object {
+            fastaFile: indexedFile,
+            indexFiles: [
+                indexedFile + ".amb",
+                indexedFile + ".ann",
+                indexedFile + ".bwt",
+                indexedFile + ".pac",
+                indexedFile + ".sa"
+            ]
+        }
+    }
+
+    runtime {
+        docker: dockerImage
+        cpu: 1
+        memory: "~{size(fasta, 'G') + 1}GiB"
+        time_minutes: timeMinutes
+    }
+
+    parameter_meta {
+        # inputs
+        fasta: {description: "Reference fasta file.", category: "required"}
+        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
+        index: {description: "The produced BWA index."}
+    }
+}

samtools.wdl

@@ -66,6 +66,53 @@ task BgzipAndIndex {
     }
 }
 
+task DictAndFaidx {
+    input {
+        File inputFile
+        String javaXmx = "2G"
+        String memory = "3GiB"
+        Int timeMinutes = 5 + ceil(size(inputFile, "GiB") * 5)
+        String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
+    }
+
+    String outputFile = basename(inputFile)
+    # Capture .fa¸ .fna and .fasta
+    String outputDict = sub(outputFile, "\.fn?as?t?a?$", "") + ".dict"
+    # This executes both dict and faidx, so indexes are co-located in the same folder.
+    command <<<
+        set -e
+        cp ~{inputFile} ~{outputFile}
+        samtools dict -o ~{outputDict}  ~{outputFile}
+        samtools faidx ~{outputFile} --fai-idx ~{outputFile}.fai
+    >>>
+
+    output {
+        File outputFasta = outputFile
+        File outputFastaDict = outputDict
+        File outputFastaFai = outputFile + ".fai"
+    }
+
+    runtime {
+        memory: memory
+        docker: dockerImage
+        time_minutes: timeMinutes
+        cpu: 1
+    }
+
+    parameter_meta {
+        # inputs
+        inputFile: {description: "The input fasta file.", category: "required"}
+        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 available to the job.", 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
+        outputFasta: {description: "Fasta file that is co-located with the indexes"}
+        outputFastaFai: {description: "Fasta index file for the outputFasta file."}
+        outputFastaDict: {description: "Sequence dictionary for the outputFasta file."}
+    }
+}
+
 task Faidx {
     input {
         File inputFile
@@ -470,7 +517,7 @@ task Sort {
 task Tabix {
     input {
         File inputFile
-        String outputFilePath = "indexed.vcf.gz"
+        String outputFilePath = basename(inputFile)
         String type = "vcf"
 
         Int timeMinutes = 1 + ceil(size(inputFile, "GiB") * 2)