error strategy enabled

AggressiveHayBale · Feb 13, 2023 · 725b460 · 725b460
1 parent c9d1559
commit 725b460
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Showing 6 changed files with 2 additions and 10 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,6 +1,5 @@
 process prokka {
     label 'prokka'
-    errorStrategy 'ignore'
     input: 
         tuple val(name), val(species), path(fasta), val(type)
     output: