diff --git a/wdl/metaMS.wdl b/wdl/metaMS.wdl index 14b8e7e..2022b61 100644 --- a/wdl/metaMS.wdl +++ b/wdl/metaMS.wdl @@ -1,48 +1,46 @@ +version 1.0 + workflow gcmsMetabolomics { - call runMetaMS -} -task runMetaMS { - - Array[File] file_paths - - File calibration_file_path - - String output_directory - String output_filename - - String output_type - - File corems_toml_path + output { + String out = runMetaMS.out + File output_file = runMetaMS.output_file + File output_metafile = runMetaMS.output_metafile + } +} - File nmdc_metadata_path +task runMetaMS { + input { + Array[File] file_paths + File calibration_file_path + String output_directory + String output_filename + String output_type + File corems_toml_path + File nmdc_metadata_path + Int jobs_count + } - Int jobs_count - command { - - metaMS run-gcms-wdl-workflow ${sep=',' file_paths} \ - ${calibration_file_path} \ - ${output_directory} \ - ${output_filename} \ - ${output_type} \ - ${corems_toml_path} \ - ${nmdc_metadata_path} \ - --jobs ${jobs_count} + metaMS run-gcms-wdl-workflow \ + ${sep=',' file_paths} \ + ${calibration_file_path} \ + ${output_directory} \ + ${output_filename} \ + ${output_type} \ + ${corems_toml_path} \ + ${nmdc_metadata_path} \ + --jobs ${jobs_count} } - + output { - String out = read_string(stdout()) File output_file = "${output_directory}/${output_filename}.${output_type}" - File output_metafile = "${output_directory}/${output_filename}.json" + File output_metafile = "${output_directory}/${output_filename}.json" } runtime { docker: "microbiomedata/metams:2.2.2" - } - -} - +} \ No newline at end of file