From 4007932baa5c57ae2407489152b4046a3923a28c Mon Sep 17 00:00:00 2001
From: "Diego Alvarez S." <dialvarezs@gmail.com>
Date: Thu, 31 Oct 2024 23:46:32 -0300
Subject: [PATCH] Add busco error strategy

---
 conf/base.config             | 2 ++
 subworkflows/local/bin_qc.nf | 5 ++---
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/conf/base.config b/conf/base.config
index 9be49eaa..128fa9f9 100644
--- 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
index b87e7998..b2f78e7b 100644
--- 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()
         }