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