make demux_metadata_only work without biosample data

Author: dpark01

pipes/WDL/workflows/demux_metadata_only.wdl

@@ -56,57 +56,61 @@ workflow demux_metadata_only {
         }
     }
 
-    #### merge biosample attribute tsvs (iff provided with more than one)
-    if (length(biosample_map_tsvs) > 1) {
-        call utils.tsv_join as biosample_map_tsv_join {
-            input:
-                input_tsvs   = biosample_map_tsvs,
-                id_col       = 'accession',
-                out_suffix   = ".tsv",
-                out_basename = "biosample-attributes-merged"
+    if(length(biosample_map_tsvs) > 0) {
+        # NCBI biosample metadata is available
+
+        #### merge biosample attribute tsvs (iff provided with more than one)
+        if (length(biosample_map_tsvs) > 1) {
+            call utils.tsv_join as biosample_map_tsv_join {
+                input:
+                    input_tsvs   = biosample_map_tsvs,
+                    id_col       = 'accession',
+                    out_suffix   = ".tsv",
+                    out_basename = "biosample-attributes-merged"
+            }
         }
-    }
-    File biosample_map_tsv = select_first(flatten([[biosample_map_tsv_join.out_tsv], biosample_map_tsvs]))
-
-    #### biosample metadata mapping
-    call ncbi.biosample_to_table {
-        input:
-            biosample_attributes_tsv = biosample_map_tsv,
-            raw_bam_filepaths        = raw_reads_unaligned_bams,
-            demux_meta_json          = meta_by_filename_json
-    }
+        File biosample_map_tsv = select_first(flatten([[biosample_map_tsv_join.out_tsv], biosample_map_tsvs]))
 
-    #### SRA submission prep
-    call ncbi.sra_meta_prep {
-        input:
-            cleaned_bam_filepaths = cleaned_reads_unaligned_bams,
-            biosample_map         = biosample_map_tsv,
-            library_metadata      = samplesheet_rename_ids.new_sheet,
-            platform              = "ILLUMINA",
-            paired                = (run_info['indexes'] == '2'),
-
-            out_name              = "sra_metadata-~{run_info['run_id']}.tsv",
-            instrument_model      = select_first(flatten([[instrument_model_user_specified],[run_info['sequencer_model']]])),
-            title                 = sra_title
-    }
+        #### biosample metadata mapping
+        call ncbi.biosample_to_table {
+            input:
+                biosample_attributes_tsv = biosample_map_tsv,
+                raw_bam_filepaths        = raw_reads_unaligned_bams,
+                demux_meta_json          = meta_by_filename_json
+        }
 
-    if(insert_demux_outputs_into_terra_tables && select_first([check_terra_env.is_running_on_terra])) {
-        call terra.upload_entities_tsv as terra_load_biosample_data {
+        #### SRA submission prep
+        call ncbi.sra_meta_prep {
             input:
-                workspace_name   = select_first([check_terra_env.workspace_name]),
-                terra_project    = select_first([check_terra_env.workspace_namespace]),
-                tsv_file         = biosample_to_table.sample_meta_tsv
+                cleaned_bam_filepaths = cleaned_reads_unaligned_bams,
+                biosample_map         = biosample_map_tsv,
+                library_metadata      = samplesheet_rename_ids.new_sheet,
+                platform              = "ILLUMINA",
+                paired                = (run_info['indexes'] == '2'),
+
+                out_name              = "sra_metadata-~{run_info['run_id']}.tsv",
+                instrument_model      = select_first(flatten([[instrument_model_user_specified],[run_info['sequencer_model']]])),
+                title                 = sra_title
+        }
+
+        if(insert_demux_outputs_into_terra_tables && select_first([check_terra_env.is_running_on_terra])) {
+            call terra.upload_entities_tsv as terra_load_biosample_data {
+                input:
+                    workspace_name   = select_first([check_terra_env.workspace_name]),
+                    terra_project    = select_first([check_terra_env.workspace_namespace]),
+                    tsv_file         = biosample_to_table.sample_meta_tsv
+            }
         }
     }
 
 
     output {
-        File        sra_metadata                             = sra_meta_prep.sra_metadata
+        File?       sra_metadata                             = sra_meta_prep.sra_metadata
 
         String      instrument_model_inferred                = select_first(flatten([[instrument_model_user_specified],[run_info['sequencer_model']]]))
 
         File?       terra_library_table                      = create_or_update_sample_tables.library_metadata_tsv
         File?       terra_sample_library_map                 = create_or_update_sample_tables.sample_membership_tsv
-        File        terra_sample_metadata                    = biosample_to_table.sample_meta_tsv
+        File?       terra_sample_metadata                    = biosample_to_table.sample_meta_tsv
     }
 }