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wdl translation to 1.0 See merge request mass-spectrometry/metams!1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,48 +1,46 @@ | ||
| version 1.0 | ||
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| workflow gcmsMetabolomics { | ||
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| call runMetaMS | ||
| } | ||
| task runMetaMS { | ||
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| Array[File] file_paths | ||
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| File calibration_file_path | ||
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| String output_directory | ||
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| String output_filename | ||
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| String output_type | ||
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| File corems_toml_path | ||
| output { | ||
| String out = runMetaMS.out | ||
| File output_file = runMetaMS.output_file | ||
| File output_metafile = runMetaMS.output_metafile | ||
| } | ||
| } | ||
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| 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 | ||
| } | ||
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| Int jobs_count | ||
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| command { | ||
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| 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 ${jobs_count} | ||
| } | ||
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| output { | ||
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| String out = read_string(stdout()) | ||
| File output_file = "${output_directory}/${output_filename}.${output_type}" | ||
| File output_metafile = "${output_directory}/${output_filename}.json" | ||
| File output_metafile = "${output_directory}/${output_filename}.json" | ||
| } | ||
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| runtime { | ||
| docker: "microbiomedata/metams:2.2.2" | ||
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| } | ||
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| } | ||
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| } |