diff --git a/.dockstore.yml b/.dockstore.yml index b693e6a43..2e5185717 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -369,6 +369,11 @@ workflows: primaryDescriptorPath: /pipes/WDL/workflows/subsample_by_metadata_with_focal.wdl testParameterFiles: - /empty.json + - name: taxid_to_nextclade + subclass: WDL + primaryDescriptorPath: /pipes/WDL/workflows/taxid_to_nextclade.wdl + testParameterFiles: + - /empty.json - name: terra_table_to_tsv subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/terra_table_to_tsv.wdl diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index a2260e077..6945d1c7d 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1,5 +1,40 @@ version 1.0 +task taxid_to_nextclade_dataset_name { + input { + String taxid + } + command <<< + python3 <>> + runtime { + docker: "python:slim" + memory: "1 GB" + cpu: 1 + disks: "local-disk " + disk_size + " LOCAL" + disk: disk_size + " GB" # TES + dx_instance_type: "mem2_ssd1_v2_x2" + maxRetries: 2 + } + output { + String nextclade_dataset_name = read_string("DATASET_NAME") + } +} + task nextclade_one_sample { meta { description: "Nextclade classification of one sample. Leaving optional inputs unspecified will use SARS-CoV-2 defaults." diff --git a/pipes/WDL/workflows/taxid_to_nextclade.wdl b/pipes/WDL/workflows/taxid_to_nextclade.wdl new file mode 100644 index 000000000..f3cae320c --- /dev/null +++ b/pipes/WDL/workflows/taxid_to_nextclade.wdl @@ -0,0 +1,15 @@ +version 1.0 + +import "../tasks/tasks_nextstrain.wdl" as nextstrain + +workflow taxid_to_nextclade { + meta { + description: "Convert taxids to a nextclade dataset name" + } + + call nextstrain.taxid_to_nextclade_dataset_name + + output { + String nextclade_dataset = taxid_to_nextclade_dataset_name.nextclade_dataset_name + } +}