Merge remote-tracking branch 'fastoma_git/main' into dev-sina

DessimozLab · Dec 1, 2023 · 3a7d146 · 3a7d146
2 parents 87714b5 + 05a0db3
commit 3a7d146
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/FastOMA/transformer.py b/FastOMA/transformer.py
@@ -16,7 +16,7 @@ def transform(self, header):
 
 class ExtractUniProtAccessionFastaHeaderTransformer(FastaHeaderTransformer):
     def __init__(self):
-        self._up_re = re.compile(r"[spup]{2}\|(?P<acc>[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})\|.*")
+        self._up_re = re.compile(r"[sptr]{2}\|(?P<acc>[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})\|.*")
 
     def transform(self, header):
         m = self._up_re.match(header)

diff --git a/conf/base.config b/conf/base.config
@@ -15,9 +15,9 @@ process {
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
     shell  = ['/bin/bash', '-euo', 'pipefail']
 
-    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
-    maxRetries    = 1
-    maxErrors     = '-1'
+    //errorStrategy = { task.exitStatus in (130..145) ? 'retry' : 'finish' }
+    errorStrategy = 'retry'
+    maxRetries    = 3
 
     withLabel:process_single {
         cpus   = { check_max( 1                   , 'cpus'    ) }