Fix busco channels and namespace in summary script

nf-core · Dec 16, 2024 · a44eb56 · a44eb56
1 parent abc1760
commit a44eb56
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Showing 2 changed files with 7 additions and 6 deletions.
diff --git a/bin/combine_tables.py b/bin/combine_tables.py
@@ -110,7 +110,7 @@ def main(args=None):
     bins = results["bin"].sort_values().reset_index(drop=True)
 
     if args.binqc_summary and args.binqc_tool == "busco":
-        busco_results = pd.read_csv(args.busco_summary, sep="\t")
+        busco_results = pd.read_csv(args.binqc_summary, sep="\t")
         busco_bins = set(busco_results["Input_file"])
 
         if set(bins) != busco_bins and len(busco_bins.intersection(set(bins))) > 0:

diff --git a/subworkflows/local/bin_qc.nf b/subworkflows/local/bin_qc.nf
@@ -88,19 +88,20 @@ workflow BIN_QC {
                 if (ch_busco_db.getSimpleName().contains('odb')) {
                     busco_lineage = ch_busco_db.getSimpleName()
                 }
-                busco_db = BUSCO_UNTAR.out.untar.map { it[1] }
+                ch_busco_db = BUSCO_UNTAR.out.untar.map { it[1] }
             }
-            else if (busco_db.isDirectory()) {
-                if (busco_db.name.matches(/odb\d+$/)) {
-                    busco_lineage = busco_db.name
+            else if (ch_busco_db.isDirectory()) {
+                if (ch_busco_db.name.matches(/odb\d+$/)) {
+                    busco_lineage = ch_busco_db.name
                 }
             }
         }
 
-        BUSCO_BUSCO(ch_bins, 'genome', busco_lineage, busco_db, [])
+        BUSCO_BUSCO(ch_bins, 'genome', busco_lineage, ch_busco_db, [])
 
         COMBINE_BINQC_TSV(BUSCO_BUSCO.out.batch_summary.map { it[1] }.collect())
 
+        qc_summary = COMBINE_BINQC_TSV.out.combined
         ch_versions = ch_versions.mix(
             BUSCO_BUSCO.out.versions.first(),
             COMBINE_BINQC_TSV.out.versions