remove deprecated task

common.wdl

@@ -134,47 +134,6 @@ task MapMd5 {
     }
 }
 
-task SampleConfigToSampleReadgroupLists {
-    input {
-        File yaml
-        String outputJson = "samples.json"
-
-        String dockerImage = "biowdl/pyyaml:3.13-py37-slim"
-    }
-
-    command <<<
-        set -e
-        mkdir -p $(dirname ~{outputJson})
-        python <<CODE
-        import json
-        import yaml
-        with open("~{yaml}", "r") as input_yaml:
-            sample_config = yaml.load(input_yaml)
-
-        sample_rg_lists = []
-        for sample in sample_config["samples"]:
-            new_sample = {"readgroups": [], "id": sample['id']}
-            for library in sample["libraries"]:
-                for readgroup in library["readgroups"]:
-                    new_readgroup = {'lib_id': library['id'], 'id': readgroup['id']}
-                    # Having a nested "reads" struct does not make any sense.
-                    new_readgroup.update(readgroup["reads"])
-                    new_sample['readgroups'].append(new_readgroup)
-            sample_rg_lists.append(new_sample)
-        sample_mod_config = {"samples": sample_rg_lists}
-        with open("~{outputJson}", "w") as output_json:
-            json.dump(sample_mod_config, output_json)
-        CODE
-    >>>
-
-    output {
-        File json = outputJson
-    }
-
-    runtime {
-        docker: dockerImage
-    }
-}
 
 task StringArrayMd5 {
     input {