tidy styles tasks

theiagen · Dec 18, 2024 · 3676e96 · 3676e96
1 parent 9b92893
commit 3676e96
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Showing 4 changed files with 2 additions and 8 deletions.
diff --git a/tasks/basecalling/task_dorado_demux.wdl b/tasks/basecalling/task_dorado_demux.wdl
@@ -11,7 +11,6 @@ task dorado_demux {
     String docker = "us-docker.pkg.dev/general-theiagen/staphb/dorado:0.8.0"
     String dorado_model_used
   }
-
   command <<< 
     set -euo pipefail
 
@@ -96,15 +95,13 @@ task dorado_demux {
     echo "### Dorado demux process completed successfully ###"
     date
   >>>
-
   output {
     Array[File] fastq_files = glob("merged_output/*.fastq.gz")
     String dorado_docker = docker
     String dorado_version = read_string("DORADO_VERSION")
     File dorado_demux_log = "dorado_demux_output.log" 
     String dorado_model_name = read_string("DORADO_MODEL_USED")
   }
-
   runtime {
     docker: docker
     cpu: cpu

diff --git a/tasks/basecalling/task_samtools_convert.wdl b/tasks/basecalling/task_samtools_convert.wdl
@@ -8,7 +8,6 @@ task samtools_convert {
     Int disk_size = 50
     String docker = "us-docker.pkg.dev/general-theiagen/staphb/samtools:1.15"
   }
-
   command <<< 
     set -euo pipefail
 
@@ -35,7 +34,6 @@ task samtools_convert {
     echo "### Listing BAM files in $bam_output ###"
     ls -lh "$bam_output"
   >>>
-
   output {
     Array[File] bam_files = glob("output/bam/*.bam")
     String samtools_version = read_string("SAMTOOLS_VERSION")

diff --git a/tasks/utilities/file_handling/task_transfer_pod5_files.wdl b/tasks/utilities/file_handling/task_transfer_pod5_files.wdl
@@ -9,9 +9,9 @@ task transfer_pod5_files {
     String docker =  "us-docker.pkg.dev/general-theiagen/cloudsdktool/google-cloud-cli:427.0.0-alpine"
   }
   command <<<
-     set -euo pipefail
+    set -euo pipefail
 
-     echo "Listing .pod5 files in ~{pod5_bucket_path}"
+    echo "Listing .pod5 files in ~{pod5_bucket_path}"
     gcloud storage ls -r "~{pod5_bucket_path}" | grep "\.pod5$" > pod5_files_list.txt
 
     # Check if any files are found

diff --git a/workflows/utilities/wf_dorado_basecalling.wdl b/workflows/utilities/wf_dorado_basecalling.wdl
@@ -28,7 +28,6 @@ workflow dorado_basecalling_workflow {
   call versioning_task.version_capture {
     input:
   }
-  # List `.pod5` files in GCS bucket
   call transfer_pod5_files_task.transfer_pod5_files as transfer_pod5 {
     input:
       pod5_bucket_path = pod5_bucket_path