Initial wdl code

h5_structs.wdl

@@ -0,0 +1,100 @@
+version development-1.1
+
+struct Sample {
+    String name
+    String primer
+    File fastq1
+    File fastq2 
+    Int i
+}
+
+struct Reference {
+    String name
+    File fasta
+}
+
+struct PrimerScheme {
+    String name
+    Array[Reference] references
+    File bed
+}
+
+struct VersionInfo {
+  String software
+  String docker
+  String version
+}
+
+struct SampleReferenceOutputs {
+    String primer_scheme_name
+    String reference_name
+    Pair[String, File] bam
+    Pair[String, File] trimmed_sorted_bam
+    Pair[String, File] trimmed_sorted_bai
+    Pair[String, File] pileup
+    Pair[String, File] consensus_fasta
+    Pair[String, File] samtools_coverage
+    Pair[String, File] samtools_stats
+    Pair[String, File] coverage_stats
+}
+
+workflow declare_structs {
+    input {
+        File bovine_texas_029328_01_UtoT_ha_fasta
+        File bovine_texas_029328_01_UtoT_fasta
+        File darwin_9_2021_h3n2_ha_h3_fasta
+        File victoria_4897_2022_h1n1_ha_h1_fasta
+        File vietnam_1203_2024_h5n1_ha_v2_fasta  
+        File human_h5_250_bed
+        File houston_bed
+        File AVRL_H5N1_250bp_bed
+    }
+    Reference vietnam_1203_2024_h5n1_ha_v2 = Reference {
+        name: "vietnam_1203_2024_h5n1_ha_v2",
+        fasta: vietnam_1203_2024_h5n1_ha_v2_fasta
+    }
+    Reference bovine_texas_029328_01_UtoT_ha = Reference {
+        name: "bovine_texas_029328_01_UtoT_ha",
+        fasta: bovine_texas_029328_01_UtoT_ha_fasta
+    }
+    Reference bovine_texas_029328_01_UtoT = Reference {
+        name: "bovine_texas_029328_01_UtoT",
+        fasta: bovine_texas_029328_01_UtoT_fasta
+    }
+    Reference darwin_9_2021_h3n2_ha_h3 = Reference {
+        name: "darwin_9_2021_h3n2_ha_h3",
+        fasta: darwin_9_2021_h3n2_ha_h3_fasta
+    }
+    Reference victoria_4897_2022_h1n1_ha_h1 = Reference {
+        name: "victoria_4897_2022_h1n1_ha_h1",
+        fasta: victoria_4897_2022_h1n1_ha_h1_fasta
+    }
+
+    PrimerScheme human_h5_250 = PrimerScheme {
+        name: "human_h5_250",
+        references:   [vietnam_1203_2024_h5n1_ha_v2, 
+                            bovine_texas_029328_01_UtoT_ha],
+        bed: human_h5_250_bed
+    }
+    PrimerScheme houston = PrimerScheme {
+        name: "houston",
+        references:  [darwin_9_2021_h3n2_ha_h3, 
+                            victoria_4897_2022_h1n1_ha_h1, 
+                            bovine_texas_029328_01_UtoT_ha],
+        bed: houston_bed
+    }
+    PrimerScheme AVRL_H5N1_250bp = PrimerScheme {
+        name: "AVRL_H5N1_250bp",
+        references: [bovine_texas_029328_01_UtoT],
+        bed: AVRL_H5N1_250bp_bed
+    }
+
+    output {
+        Array[PrimerScheme] primer_schemes = [human_h5_250, houston, AVRL_H5N1_250bp] 
+        Array[Reference] references = [vietnam_1203_2024_h5n1_ha_v2, 
+                                        bovine_texas_029328_01_UtoT_ha, 
+                                        darwin_9_2021_h3n2_ha_h3, 
+                                        victoria_4897_2022_h1n1_ha_h1,
+                                        bovine_texas_029328_01_UtoT]
+    }
+}