diff --git a/tasks/basecalling/task_dorado_demux.wdl b/tasks/basecalling/task_dorado_demux.wdl index 6fdd3febf..dc7200ca2 100644 --- 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 @@ -96,7 +95,6 @@ task dorado_demux { echo "### Dorado demux process completed successfully ###" date >>> - output { Array[File] fastq_files = glob("merged_output/*.fastq.gz") String dorado_docker = docker @@ -104,7 +102,6 @@ task dorado_demux { 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 index decb4b06d..852d404aa 100644 --- 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 index 07326d5e7..3c82a0bb3 100644 --- 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 index 33da91b1b..1c2fe3487 100644 --- 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