From 725b46081e25b51f0fc4b68dc1f04fdcd22dbb08 Mon Sep 17 00:00:00 2001
From: Mateusz <mateusz.jun@gmail.com>
Date: Mon, 13 Feb 2023 14:26:58 +0100
Subject: [PATCH] error strategy enabled

---
 nextflow.config               | 7 ++-----
 workflows/process/analysis.nf | 1 -
 workflows/process/bakta.nf    | 1 -
 workflows/process/eggnog.nf   | 1 -
 workflows/process/pgap.nf     | 1 -
 workflows/process/prokka.nf   | 1 -
 6 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index e7a5259..3391d30 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -89,11 +89,8 @@ profiles {
     includeConfig 'configs/nodes.config'
 
     // cloud error strategy
-    //process.errorStrategy = { task.exitStatus in [10,14,143,137,104,134,139] ? 'retry' : 'ignore' }
-    //process.maxRetries = 3
+    process.errorStrategy = { task.exitStatus in [10,14,143,137,104,134,139] ? 'retry' : 'ignore' }
+    process.maxRetries = 3
     }
 
-// test_profile
-//    test {
-//    }
 }
diff --git a/workflows/process/analysis.nf b/workflows/process/analysis.nf
index b2d56c5..2eac41b 100644
--- a/workflows/process/analysis.nf
+++ b/workflows/process/analysis.nf
@@ -1,6 +1,5 @@
 process analysis {
     label 'r' 
-    errorStrategy 'ignore'
     input:
         //tuple val(id), path(prokka_faa), path(prokka_gff), path(bakta_faa), path(bakta_gff), path(eggnog_faa), path(eggnog_gff), path(pgap_faa), path(pgap_gff)
         tuple val(id), val(type1), path(prokka_1), path(prokka_2), val(type2), path(bakta_1), path(bakta_2), val(type3), path(eggnog_1), path(eggnog_2), val(type4), path(pgap_1), path(pgap_2)
diff --git a/workflows/process/bakta.nf b/workflows/process/bakta.nf
index e28c519..c650163 100644
--- a/workflows/process/bakta.nf
+++ b/workflows/process/bakta.nf
@@ -16,7 +16,6 @@ process bakta_database {
 
 process bakta {
     label 'bakta'
-    errorStrategy 'ignore'
     input: 
         tuple val(name), val(species), path(fasta), val(type)
         path(bakta_db_dir)
diff --git a/workflows/process/eggnog.nf b/workflows/process/eggnog.nf
index 145963c..376ca87 100644
--- a/workflows/process/eggnog.nf
+++ b/workflows/process/eggnog.nf
@@ -18,7 +18,6 @@ process eggnog_database {
 
 process eggnog {
     label 'eggnog'
-    errorStrategy 'ignore'
     input:
         tuple val(name), val(species), path(fasta), val(type)
         path(eggnog_db_dir)
diff --git a/workflows/process/pgap.nf b/workflows/process/pgap.nf
index 6f97c45..1851c1d 100644
--- a/workflows/process/pgap.nf
+++ b/workflows/process/pgap.nf
@@ -19,7 +19,6 @@ process pgap_database {
 
 process pgap {
     label 'pgap'
-    errorStrategy 'ignore'
     input: 
         tuple val(name), val(species), path(fasta), val(type)
         path(pgap_db)
diff --git a/workflows/process/prokka.nf b/workflows/process/prokka.nf
index 328cbb5..6a170f1 100755
--- a/workflows/process/prokka.nf
+++ b/workflows/process/prokka.nf
@@ -1,6 +1,5 @@
 process prokka {
     label 'prokka'
-    errorStrategy 'ignore'
     input: 
         tuple val(name), val(species), path(fasta), val(type)
     output: