nf-core · ewels · Feb 5, 2023 · Jan 24, 2023 · Jan 30, 2023 · Feb 1, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,7 @@
 
 - Turn on automatic clean up of intermediate files in `work/` on successful pipeline completion in full-test config ([#2163](https://github.com/nf-core/tools/pull/2163)) [Contributed by @jfy133]
 - Add documentation to `usage.md` on how to use `params.yml` files, based on nf-core/ampliseq text ([#2173](https://github.com/nf-core/tools/pull/2173/)) [Contributed by @jfy133, @d4straub]
+- Make jobs automatically resubmit for a much wider range of exit codes (now `104` and `130..145`)
 
 ### Linting
 

diff --git a/nf_core/bump_version.py b/nf_core/bump_version.py
@@ -133,12 +133,10 @@ def update_file_version(filename, pipeline_obj, patterns):
 
     replacements = []
     for pattern in patterns:
-
         found_match = False
 
         newcontent = []
         for line in content.splitlines():
-
             # Match the pattern
             matches_pattern = re.findall(rf"^.*{pattern[0]}.*$", line)
             if matches_pattern:

diff --git a/nf_core/create.py b/nf_core/create.py
@@ -283,7 +283,6 @@ def render_template(self):
 
         # Set the paths to skip according to customization
         for template_fn_path_obj in template_files:
-
             template_fn_path = str(template_fn_path_obj)
 
             # Skip files that are in the self.skip_paths list

diff --git a/nf_core/download.py b/nf_core/download.py
@@ -506,7 +506,6 @@ def get_singularity_images(self):
                 containers_download = []
                 containers_pull = []
                 for container in self.containers:
-
                     # Fetch the output and cached filenames for this container
                     out_path, cache_path = self.singularity_image_filenames(container)
 

diff --git a/nf_core/launch.py b/nf_core/launch.py
@@ -98,7 +98,6 @@ def __init__(
         self.cli_launch = True
 
     def launch_pipeline(self):
-
         # Prompt for pipeline if not supplied and no web launch ID
         if self.pipeline is None and self.web_id is None:
             launch_type = questionary.select(
@@ -461,7 +460,6 @@ def prompt_group(self, group_id, group_obj):
         answers = {}
         error_msgs = []
         while not while_break:
-
             if len(error_msgs) == 0:
                 self.print_param_header(group_id, group_obj, True)
 
@@ -698,7 +696,6 @@ def build_command(self):
 
         # Pipeline parameters
         if len(self.schema_obj.input_params) > 0:
-
             # Write the user selection to a file and run nextflow with that
             if self.use_params_file:
                 dump_json_with_prettier(self.params_out, self.schema_obj.input_params)

diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
@@ -434,7 +434,6 @@ def format_result(test_results):
             )
 
     def _print_summary(self):
-
         # Summary table
         summary_colour = "red" if len(self.failed) > 0 else "green"
         table = Table(box=rich.box.ROUNDED, style=summary_colour)

diff --git a/nf_core/lint/files_unchanged.py b/nf_core/lint/files_unchanged.py
@@ -147,7 +147,6 @@ def _tf(file_path):
 
     # Files that must be completely unchanged from template
     for files in files_exact:
-
         # Ignore if file specified in linting config
         ignore_files = self.lint_config.get("files_unchanged", [])
         if any([f in ignore_files for f in files]):
@@ -177,7 +176,6 @@ def _tf(file_path):
 
     # Files that can be added to, but that must contain the template contents
     for files in files_partial:
-
         # Ignore if file specified in linting config
         ignore_files = self.lint_config.get("files_unchanged", [])
         if any([f in ignore_files for f in files]):

diff --git a/nf_core/lint/template_strings.py b/nf_core/lint/template_strings.py
@@ -24,7 +24,6 @@ def template_strings(self):
     # Loop through files, searching for string
     num_matches = 0
     for fn in self.files:
-
         # Skip binary files
         binary_ftypes = ["image", "application/java-archive"]
         (ftype, encoding) = mimetypes.guess_type(fn)

diff --git a/nf_core/list.py b/nf_core/list.py
@@ -328,7 +328,6 @@ def get_local_nf_workflow_details(self):
         """Get full details about a local cached workflow"""
 
         if self.local_path is None:
-
             # Try to guess the local cache directory
             if len(os.environ.get("NXF_ASSETS", "")) > 0:
                 nf_wfdir = os.path.join(os.environ.get("NXF_ASSETS"), self.full_name)

diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
@@ -187,7 +187,6 @@ def bump_module_version(self, module):
                 found_match = False
                 newcontent = []
                 for line in content.splitlines():
-
                     # Match the pattern
                     matches_pattern = re.findall(rf"^.*{pattern[0]}.*$", line)
                     if matches_pattern:

diff --git a/nf_core/pipeline-template/conf/base.config b/nf_core/pipeline-template/conf/base.config
@@ -15,7 +15,7 @@ process {
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
 
-    errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 

diff --git a/nf_core/utils.py b/nf_core/utils.py
@@ -872,7 +872,6 @@ def get_repo_releases_branches(pipeline, wfs):
     # Repo is a nf-core pipeline
     for wf in wfs.remote_workflows:
         if wf.full_name == pipeline or wf.name == pipeline:
-
             # Set to full name just in case it didn't have the nf-core/ prefix
             pipeline = wf.full_name
 
@@ -883,7 +882,6 @@ def get_repo_releases_branches(pipeline, wfs):
     # Arbitrary GitHub repo
     else:
         if pipeline.count("/") == 1:
-
             # Looks like a GitHub address - try working with this repo
             log.debug(
                 f"Pipeline '{pipeline}' not in nf-core, but looks like a GitHub address - fetching releases from API"

diff --git a/tests/test_download.py b/tests/test_download.py
@@ -18,7 +18,6 @@
 
 
 class DownloadTest(unittest.TestCase):
-
     #
     # Tests for 'get_release_hash'
     #

diff --git a/tests/test_test_utils.py b/tests/test_test_utils.py
@@ -33,7 +33,6 @@ def test_tmp_folder_does_not_exist_after():
 
 
 def test_set_wd():
-
     with tempfile.TemporaryDirectory() as tmpdirname:
         with set_wd(tmpdirname):
             context_wd = Path().resolve()
-Original file line number
+Diff line change
@@ Expand Up / @@ -18,7 +18,6 @@ @@
     class DownloadTest(unittest.TestCase):
         #
         # Tests for 'get_release_hash'
         #
@@ Expand Down @@