Merge pull request #572 from broadinstitute/dp-demux-fix

bugfix: demux_deplete with biosample attributes
broadinstitute · Nov 25, 2024 · b8bb70b · b8bb70b
2 parents 6c59d05 + 9017a80
commit b8bb70b
Showing 1 changed file with 33 additions and 31 deletions.
diff --git a/pipes/WDL/workflows/demux_deplete.wdl b/pipes/WDL/workflows/demux_deplete.wdl
@@ -26,7 +26,7 @@ workflow demux_deplete {
         Boolean      insert_demux_outputs_into_terra_tables=false
 
         File?        sample_rename_map
-        Array[File]? biosample_map_tsvs
+        Array[File]  biosample_map_tsvs = []
         Int          min_reads_per_bam = 100
 
         String?      instrument_model_user_specified
@@ -183,22 +183,43 @@ workflow demux_deplete {
         Pair[String,Int] count_cleaned = (basename(raw_reads, '.bam'), read_count_post_depletion)
     }
 
-    if (length(flatten(select_all([biosample_map_tsvs]))) > 0) {
+    if(insert_demux_outputs_into_terra_tables) {
+        call terra.check_terra_env
+
+        if(check_terra_env.is_running_on_terra) {
+            call terra.create_or_update_sample_tables {
+              input:
+                flowcell_run_id     = illumina_demux.run_info[0]['run_id'],
+                workspace_name      = check_terra_env.workspace_name,
+                workspace_namespace = check_terra_env.workspace_namespace,
+
+                raw_reads_unaligned_bams     = flatten(illumina_demux.raw_reads_unaligned_bams),
+                cleaned_reads_unaligned_bams = select_all(cleaned_bam_passing),
+                meta_by_filename_json        = meta_filename.merged_json,
+                read_counts_raw_json         = write_json(count_raw),
+                read_counts_cleaned_json     = write_json(count_cleaned)
+            }
+        }
+    }
+
+
+    if (length(biosample_map_tsvs) > 0) {
         #### merge biosample attribute tsvs (iff provided with more than one)
-        if (length(flatten(select_all([biosample_map_tsvs]))) > 1) {
+        if (length(biosample_map_tsvs) > 1) {
             call utils.tsv_join as biosample_map_tsv_join {
                 input:
-                    input_tsvs   = flatten([select_first([biosample_map_tsvs,[]])]),
+                    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 = select_first([biosample_map_tsv_join.out_tsv, biosample_map_tsvs]),
+                biosample_attributes_tsv = biosample_map_tsv,
                 cleaned_bam_filepaths    = select_all(cleaned_bam_passing),
                 demux_meta_json          = meta_filename.merged_json
         }
@@ -207,7 +228,7 @@ workflow demux_deplete {
         call ncbi.sra_meta_prep {
             input:
                 cleaned_bam_filepaths = select_all(cleaned_bam_passing),
-                biosample_map         = select_first([biosample_map_tsv_join.out_tsv, biosample_map_tsvs]),
+                biosample_map         = biosample_map_tsv,
                 library_metadata      = samplesheet_rename_ids.new_sheet,
                 platform              = "ILLUMINA",
                 paired                = (illumina_demux.run_info[0]['indexes'] == '2'),
@@ -216,32 +237,13 @@ workflow demux_deplete {
                 instrument_model      = select_first(flatten([[instrument_model_user_specified],[illumina_demux.run_info[0]['sequencer_model']]])),
                 title                 = select_first([sra_title])
         }
-    }
 
-    if(insert_demux_outputs_into_terra_tables) {
-        call terra.check_terra_env
-
-        if(check_terra_env.is_running_on_terra) {
-            call terra.create_or_update_sample_tables {
-              input:
-                flowcell_run_id     = illumina_demux.run_info[0]['run_id'],
-                workspace_name      = check_terra_env.workspace_name,
-                workspace_namespace = check_terra_env.workspace_namespace,
-
-                raw_reads_unaligned_bams     = flatten(illumina_demux.raw_reads_unaligned_bams),
-                cleaned_reads_unaligned_bams = select_all(cleaned_bam_passing),
-                meta_by_filename_json        = meta_filename.merged_json,
-                read_counts_raw_json         = write_json(count_raw),
-                read_counts_cleaned_json     = write_json(count_cleaned)
-            }
-
-            if (length(flatten(select_all([biosample_map_tsvs]))) > 0) {
-                call terra.upload_entities_tsv as terra_load_biosample_data {
-                    input:
-                        workspace_name   = check_terra_env.workspace_name,
-                        terra_project    = check_terra_env.workspace_namespace,
-                        tsv_file         = select_first([biosample_to_table.sample_meta_tsv])
-                }
+        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
             }
         }
     }