Add a WDL to run ExpansionHunter on multiple samples (#253)

* Add a WDL to run ExpansionHunter on multiple inputs.

* Add output prefix arg, defaults to input filename.

* Rename docker var in EH WDLs to 'expansion_hunter_docker'

* Add an optional list of per sample output prefix.

Author: VJalili

wdl/ExpansionHunter.wdl

@@ -20,7 +20,8 @@ workflow ExpansionHunter {
         File reference_fasta
         File? reference_fasta_index
         File variant_catalog
-        String docker_file
+        File? output_prefix
+        String expansion_hunter_docker
         RuntimeAttr? runtime_attr
     }
 
@@ -35,14 +36,24 @@ workflow ExpansionHunter {
         reference_fasta_index,
         reference_fasta + ".fai"])
 
+    String output_prefix_ =
+        if defined(output_prefix) then
+            select_first([output_prefix])
+        else
+            if is_bam then
+                basename(bam_or_cram, ".bam")
+            else
+                basename(bam_or_cram, ".cram")
+
     call RunExpansionHunter {
         input:
             bam_or_cram = bam_or_cram,
             bam_or_cram_index = bam_or_cram_index_,
             reference_fasta = reference_fasta,
             reference_fasta_index = reference_fasta_index_,
             variant_catalog = variant_catalog,
-            docker_file = docker_file,
+            output_prefix = output_prefix_,
+            expansion_hunter_docker = expansion_hunter_docker,
             runtime_attr_override = runtime_attr,
     }
 
@@ -60,12 +71,11 @@ task RunExpansionHunter {
         File reference_fasta
         File reference_fasta_index
         File variant_catalog
-        String docker_file
+        String output_prefix
+        String expansion_hunter_docker
         RuntimeAttr? runtime_attr_override
     }
 
-    String output_prefix = "output"
-
     output {
         File json = "${output_prefix}.json"
         File vcf = "${output_prefix}.vcf"
@@ -99,7 +109,7 @@ task RunExpansionHunter {
         runtime_attr_str_profile_default])
 
     runtime {
-        docker: docker_file
+        docker: expansion_hunter_docker
         cpu: runtime_attr.cpu_cores
         memory: runtime_attr.mem_gb + " GiB"
         disks: "local-disk " + runtime_attr.disk_gb + " HDD"

wdl/ExpansionHunterScatter.wdl

@@ -0,0 +1,58 @@
+version 1.0
+
+import "Structs.wdl"
+import "ExpansionHunter.wdl" as ExpansionHunter
+
+workflow ExpansionHunterScatter {
+
+    input {
+        Array[File] bams_or_crams
+        Array[File]? bams_or_crams_indexes
+        Array[String]? sample_ids
+        File reference_fasta
+        File? reference_fasta_index
+        File variant_catalog
+        String expansion_hunter_docker
+        RuntimeAttr? runtime_attr
+    }
+
+    scatter (i in range(length(bams_or_crams))) {
+        File bam_or_cram_ = bams_or_crams[i]
+        Boolean is_bam =
+            basename(bam_or_cram_, ".bam") + ".bam" == basename(bam_or_cram_)
+        File bam_or_cram_index_ =
+            if defined(bams_or_crams_indexes) then
+                select_first([bams_or_crams_indexes])[i]
+            else
+                bam_or_cram_ + if is_bam then ".bai" else ".crai"
+        File reference_fasta_index_ = select_first([
+            reference_fasta_index, reference_fasta + ".fai"])
+
+        String output_prefix =
+            if defined(sample_ids) then
+                select_first([sample_ids])[i]
+            else
+                if is_bam then
+                    basename(bam_or_cram_, ".bam")
+                else
+                    basename(bam_or_cram_, ".cram")
+
+        call ExpansionHunter.ExpansionHunter as expanionHunter {
+            input:
+                bam_or_cram=bam_or_cram_,
+                bam_or_cram_index=bam_or_cram_index_,
+                reference_fasta=reference_fasta,
+                reference_fasta_index=reference_fasta_index_,
+                variant_catalog=variant_catalog,
+                output_prefix=output_prefix,
+                expansion_hunter_docker=expansion_hunter_docker,
+                runtime_attr=runtime_attr
+        }
+    }
+
+    output {
+        Array[File] jsons = expanionHunter.json
+        Array[File] vcfs = expanionHunter.vcf
+        Array[File] overlapping_reads = expanionHunter.overlapping_reads
+    }
+}