From c84ce51cc75bf56af80c2749e5bf2cf39cd1b5b7 Mon Sep 17 00:00:00 2001
From: Sage Wright <sage.wright@theiagen.com>
Date: Wed, 20 Sep 2023 16:07:15 +0000
Subject: [PATCH] apply style guidelines

---
 tasks/species_typing/task_clockwork.wdl | 37 +++++++++++--------------
 1 file changed, 16 insertions(+), 21 deletions(-)

diff --git a/tasks/species_typing/task_clockwork.wdl b/tasks/species_typing/task_clockwork.wdl
index 8c7d2f680..6e0d027f9 100644
--- a/tasks/species_typing/task_clockwork.wdl
+++ b/tasks/species_typing/task_clockwork.wdl
@@ -1,53 +1,48 @@
 version 1.0
 
 task clockwork_decon_reads {
-  # Inputs
   input {
     File read1
-    File? read2
+    File read2
     String samplename
     Int disk_size = 200
     Int cpu = 16
     Int mem = 64
     String docker = "us-docker.pkg.dev/general-theiagen/cdcgov/varpipe_wgs_with_refs:2bc7234074bd53d9e92a1048b0485763cd9bbf6f4d12d5a1cc82bfec8ca7d75e"
-    }
-
+  }
   command <<<
-    # Print and save date
-    date | tee DATE
-
     # Print and save version
     clockwork version > VERSION
 
     # Map reads to the clockwork reference
     clockwork map_reads \
-    --unsorted_sam ~{samplename} /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa \
-    "~{samplename}.sam" \
-    ~{read1} \
-    ~{read2}
+      --unsorted_sam ~{samplename} /varpipe_wgs/tools/clockwork-0.11.3/OUT/ref.fa \
+      "~{samplename}.sam" \
+      ~{read1} \
+      ~{read2}
 
     # Remove contaminants (reads that map with high identity to non-MTB sequences)
     clockwork remove_contam \
-    /varpipe_wgs/tools/clockwork-0.11.3/OUT/remove_contam_metadata.tsv \
-    "~{samplename}.sam" \
-    "~{samplename}_outfile_read_counts" \
-    "./clockwork_cleaned_~{samplename}_R1.fastq.gz" \
-    "./clockwork_cleaned_~{samplename}_R2.fastq.gz"
+      /varpipe_wgs/tools/clockwork-0.11.3/OUT/remove_contam_metadata.tsv \
+      "~{samplename}.sam" \
+      "~{samplename}_outfile_read_counts" \
+      "clockwork_cleaned_~{samplename}_R1.fastq.gz" \
+      "clockwork_cleaned_~{samplename}_R2.fastq.gz"
 
     # Clean up files
     rm "~{samplename}.sam"
-
   >>>
   output {
-    File clockwork_cleaned_read1 = "./clockwork_cleaned_~{samplename}_R1.fastq.gz"
-    File clockwork_cleaned_read2 = "./clockwork_cleaned_~{samplename}_R2.fastq.gz"
+    File clockwork_cleaned_read1 = "clockwork_cleaned_~{samplename}_R1.fastq.gz"
+    File clockwork_cleaned_read2 = "clockwork_cleaned_~{samplename}_R2.fastq.gz"
   }
   runtime {
     docker: docker
-    memory: "~{mem} GB"
+    memory: mem + " GB"
     cpu: cpu
     disks: "local-disk " + disk_size + " SSD"
     disk: disk_size + " GB"
-    maxRetries: 3 
+    maxRetries: 3
+    preemptible: 1
   }
 }
\ No newline at end of file