wdl to extract chr:pos:ref:alt from an array of VCF files

.dockstore.yml

@@ -5,13 +5,6 @@ workflows:
      primaryDescriptorPath: /bcftools_stats.wdl
      testParameterFiles:
          - /bcftools_stats.json
-   - name: check_vcf_samples
+   - name: extract_vcf_ids
      subclass: WDL
-     primaryDescriptorPath: /check_vcf_samples.wdl
-     testParameterFiles:
-         - /check_vcf_samples.json
-   - name: test_data_tables
-     subclass: WDL
-     primaryDescriptorPath: /test_data_tables.wdl
-     testParameterFiles:
-         - /test_data_tables.json
+     primaryDescriptorPath: /extract_vcf_ids.wdl

extract_vcf_ids.wdl

@@ -0,0 +1,64 @@
+version 1.0
+
+workflow extract_vcf_ids {
+    input {
+        Array[File] vcf_file
+    }
+
+    scatter (f in vcf_file) {
+        call bcftools_query {
+            input: vcf_file = f
+        }
+    }
+
+    call concat_files {
+        input: files = bcftools_query.variant_file
+    }
+
+    output {
+        File variant_file = concat_files.output_file
+    }
+
+     meta {
+          author: "Stephanie Gogarten"
+          email: "[email protected]"
+     }
+}
+
+
+task bcftools_query {
+    input {
+        File vcf_file
+    }
+
+    command <<<
+        bcftools query -f '%CHROM:%POS:%REF:%ALT\n' ~{vcf_file} > variants.txt
+    >>>
+
+    output {
+        File variant_file = "variants.txt"
+    }
+
+    runtime {
+        docker: "staphb/bcftools:1.16"
+    }
+}
+
+
+task concat_files {
+    input {
+        Array[File] files
+    }
+
+    command <<<
+        cat ~{sep=' ' files} > concat.txt
+    >>>
+
+    output {
+        File output_file = "concat.txt"
+    }
+
+    runtime {
+        docker: "staphb/bcftools:1.16"
+    }
+}