Last fixes to get gtdb and bin summary working

nf-core · Jan 8, 2025 · d60ae40 · d60ae40
1 parent 3d4ba8b
commit d60ae40
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/subworkflows/local/bin_qc.nf b/subworkflows/local/bin_qc.nf
@@ -196,7 +196,7 @@ workflow BIN_QC {
 
     // Combine QC summaries (same process for all tools)
     CONCAT_BINQC_TSV(qc_summaries, 'tsv', 'tsv')
-    qc_summary = CONCAT_BINQC_TSV.out.csv
+    qc_summary = CONCAT_BINQC_TSV.out.csv.map { _meta, summary -> summary }
     ch_versions = ch_versions.mix(CONCAT_BINQC_TSV.out.versions)
 
     emit:

diff --git a/subworkflows/local/gtdbtk.nf b/subworkflows/local/gtdbtk.nf
@@ -22,16 +22,16 @@ workflow GTDBTK {
     ]
 
     ch_bin_metrics = bin_qc_summary
-        .map { _meta, summary -> summary }
         .splitCsv(header: true, sep: '\t')
         .map { row -> qc_columns[params.binqc_tool].collect { col -> row[col] } }
         .filter { row -> row[1] != '' }
         .map { row ->
-            row = row[0] + row[1..2].collect { value -> Double.parseDouble(value) }
+            row = [row[0]] + row[1..2].collect { value -> Double.parseDouble(value) }
             // CheckM / CheckM2 removes the .fa extension from the bin name
             if (params.binqc_tool in ['checkm', 'checkm2']) {
-                row[1] = row[1] + '.fa'
+                row[0] = row[0] + '.fa'
             }
+            row
         }
 
     // Filter bins based on collected metrics: completeness, contamination