BCFTools Sort task (#155)

Co-authored-by: TOLGA <ayazsevent@email.chop.edu>

bcftools/Sort.wdl

@@ -0,0 +1,65 @@
+version 1.0
+# -------------------------------------------------------------------------------------------------
+# Package Name: bcftools sort
+# Task Summary: sort VCF file
+# Tool Name: bcftools sort
+# Documentation:
+#  * https://https://samtools.github.io/bcftools/bcftools.html
+# -------------------------------------------------------------------------------------------------
+
+
+task BCFToolsSort {
+  input {
+    # Tools
+    File ? bcftools
+
+    # Inputs
+    File input_file
+    String sample_id
+    String ? userString
+    String filename_prefix = ""
+
+    # Run time variables
+    Array[String] modules = []
+    Float memory = 4
+    Int cpu = 1
+
+    # Output file names
+    String output_filename = sample_id + filename_prefix + ".sorted.vcf"
+  }
+
+  command {
+    set -Eeuxo pipefail;
+
+    for MODULE in ~{sep=' ' modules}; do
+      module load $MODULE
+    done;
+
+    ~{default="bcftools" bcftools} sort \
+      ~{userString} \
+      -o ~{output_filename} \
+      ~{input_file};
+  }
+
+  output {
+    File output_file = "~{output_filename}"
+  }
+
+  runtime {
+    memory: memory + " GB"
+    cpu: cpu
+  }
+
+  parameter_meta {
+    sample_id: "sample id"
+    bcftools: "bcftools executable."
+    input_file: "VCF file"
+  }
+
+  meta {
+    author: "Tolga Ayazseven"
+    email: "ayazsevent@email.chop.edu"
+    bcftools_version: "1.9"
+    version: "1.0.0"
+  }
+}