Merge pull request #275 from broadinstitute/dp-drsfix

correct inference of illumina run ID
broadinstitute · Apr 30, 2021 · 730cd1a · 730cd1a
2 parents 4b0a952 + ff693d6
commit 730cd1a
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/pipes/WDL/workflows/demux_deplete.wdl b/pipes/WDL/workflows/demux_deplete.wdl
@@ -51,8 +51,6 @@ workflow demux_deplete {
         }
     }
 
-    String  flowcell_id   = basename(basename(basename(basename(flowcell_tgz, ".gz"), ".zst"), ".tar"), ".tgz")
-
     #### demux each lane (rename samples if requested)
     scatter(lane_sheet in zip(range(length(samplesheets)), samplesheets)) {
         call demux.samplesheet_rename_ids {
@@ -115,7 +113,7 @@ workflow demux_deplete {
                 library_metadata      = samplesheet_rename_ids.new_sheet,
                 platform              = "ILLUMINA",
                 paired                = (illumina_demux.run_info[0]['indexes'] == '2'),
-                out_name              = "sra_metadata-~{flowcell_id}.tsv",
+                out_name              = "sra_metadata-~{illumina_demux.run_info[0]['run_id']}.tsv",
                 instrument_model      = select_first([instrument_model]),
                 title                 = select_first([sra_title])
         }
@@ -163,7 +161,10 @@ workflow demux_deplete {
         File        multiqc_report_cleaned                   = multiqc_cleaned.multiqc_report
         File        spikein_counts                           = spike_summary.count_summary
         
-        String      run_date                                 = illumina_demux.run_info[0]['run_start_date']
+        String             run_date                          = illumina_demux.run_info[0]['run_start_date']
+        Map[String,String] run_info                          = illumina_demux.run_info[0]
+        File               run_info_json                     = illumina_demux.run_info_json[0]
+        String             run_id                            = illumina_demux.run_info[0]['run_id']
         
         String      demux_viral_core_version                 = illumina_demux.viralngs_version[0]
     }

diff --git a/pipes/WDL/workflows/sarscov2_illumina_full.wdl b/pipes/WDL/workflows/sarscov2_illumina_full.wdl
@@ -60,7 +60,6 @@ workflow sarscov2_illumina_full {
     }
     Int     taxid         = 2697049
     String  gisaid_prefix = 'hCoV-19/'
-    String  flowcell_id   = basename(basename(basename(basename(flowcell_tgz, ".gz"), ".zst"), ".tar"), ".tgz")
 
     # merge biosample attributes tables
     call utils.tsv_join as biosample_merge {
@@ -78,6 +77,7 @@ workflow sarscov2_illumina_full {
             instrument_model = instrument_model,
             sra_title        = sra_title
     }
+    String  flowcell_id = demux_deplete.run_id
 
     ### gather data by biosample
     call read_utils.group_bams_by_sample {