Add busco error strategy

nf-core · Nov 1, 2024 · 4007932 · 4007932
1 parent da52285
commit 4007932
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -156,9 +156,11 @@ process {
     withName: MAG_DEPTHS {
         memory = { 16.GB * task.attempt }
     }
+    //BUSCO can fail when there are no hits
     withName: BUSCO {
         cpus   = { 8 * task.attempt }
         memory = { 20.GB * task.attempt }
+        errorStrategy = { task.exitStatus in (130..145)  ? 'retry' : task.exitStatus == 1 ? 'ignore' : 'finish' }
     }
     withName: MAXBIN2 {
         errorStrategy = { task.exitStatus in [1, 255] ? 'ignore' : 'retry' }

diff --git a/subworkflows/local/bin_qc.nf b/subworkflows/local/bin_qc.nf
@@ -20,7 +20,7 @@ workflow BIN_QC {
     ch_bins        // [ [ meta] , fasta           ], input bins (mandatory)
     ch_checkm_db   // [ db                        ], presupplied CheckM database (optional)
     ch_checkm2_db  // [ [meta]  , db              ], presupplied CheckM2 database (optional)
-    ch_busco_db    // [ db                        ], presupplied BUSCO database (optional)
+    ch_busco_db    // [ [meta]  , db              ], presupplied BUSCO database (optional)
     ch_gunc_db     // [ db                        ], presupplied GUNC database (optional)
 
     main:
@@ -57,8 +57,7 @@ workflow BIN_QC {
         else {
             // Set BUSCO database to empty to allow for --auto-lineage
             ch_db_for_busco = Channel
-                .of([])
-                .map { _empty_db -> [[lineage: ''], []] }
+                .of([[lineage: ''], []])
                 .collect()
         }