From 61340701d2af86576975d48e0b7f66aa6c629d99 Mon Sep 17 00:00:00 2001
From: fraser-combe <frascom@hotmail.com>
Date: Thu, 7 Nov 2024 15:34:50 -0600
Subject: [PATCH] move stray bracket

---
 tasks/basecalling/task_dorado_basecall.wdl    |  3 ++-
 tasks/basecalling/task_samtools_convert.wdl   |  2 ++
 .../data_import/wf_update_srr_metadata.wdl    | 22 -------------------
 3 files changed, 4 insertions(+), 23 deletions(-)
 delete mode 100644 workflows/utilities/data_import/wf_update_srr_metadata.wdl

diff --git a/tasks/basecalling/task_dorado_basecall.wdl b/tasks/basecalling/task_dorado_basecall.wdl
index 424a9d644..de13f36f1 100644
--- a/tasks/basecalling/task_dorado_basecall.wdl
+++ b/tasks/basecalling/task_dorado_basecall.wdl
@@ -47,7 +47,8 @@ task basecall {
     disks:  "local-disk " + disk_size + " SSD"
     disk: disk_size + " GB"
     gpuCount: 1
-    gpuType: "nvidia-tesla-t4"  }
+    gpuType: "nvidia-tesla-t4"  
     preemptible: 0
     maxRetries: 1
+    }
 }
diff --git a/tasks/basecalling/task_samtools_convert.wdl b/tasks/basecalling/task_samtools_convert.wdl
index 7e1dc184b..3a426f66d 100644
--- a/tasks/basecalling/task_samtools_convert.wdl
+++ b/tasks/basecalling/task_samtools_convert.wdl
@@ -37,5 +37,7 @@ task samtools_convert {
     cpu: cpu
     memory: "~{memory} GB"
     disks: "local-disk ~{disk_size} SSD"
+    preemptible: 0
+    maxRetries: 1
   }
 }
diff --git a/workflows/utilities/data_import/wf_update_srr_metadata.wdl b/workflows/utilities/data_import/wf_update_srr_metadata.wdl
deleted file mode 100644
index 9a62c9619..000000000
--- a/workflows/utilities/data_import/wf_update_srr_metadata.wdl
+++ /dev/null
@@ -1,22 +0,0 @@
-version 1.0
-
-import "../../../tasks/utilities/data_handling/task_fetch_srr_metadata.wdl" as srr_task
-
-workflow wf_retrieve_srr {
-  meta {
-    description: "This workflow retrieves the Sequence Read Archive (SRA) accession (SRR) associated with a given sample accession. It uses the fastq-dl tool to fetch metadata from SRA and outputs the SRR accession that can be used for downstream analysis."
-  }
-  input {
-    String sample_accession  
-    String retrieve_srr_docker = "us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0"
-  }
-
-  call srr_task.fetch_srr_metadata {
-    input:
-      sample_accession = sample_accession,  
-      docker = retrieve_srr_docker
-  }
-  output {
-    String srr_accession = fetch_srr_metadata.srr_accession 
-  }
-}
\ No newline at end of file