bactopia 2.1.3__tar.gz → 2.1.4__tar.gz

{bactopia-2.1.3 → bactopia-2.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bactopia
-Version: 2.1.3
+Version: 2.1.4
 Summary: A Python package for working with Bactopia
 License: MIT
 License-File: LICENSE

{bactopia-2.1.3 → bactopia-2.1.4}/bactopia/lint/rules/module_rules.py

@@ -139,11 +139,11 @@ def rule_m004(component: str, ctx: dict) -> list[LintResult]:
 
 
 def rule_m005(component: str, ctx: dict) -> list[LintResult]:
-    """nextflow.preview.types = true present."""
+    """nextflow.enable.types = true present."""
     rid = "M005"
     if ctx["structure"]["has_types_preview"]:
-        return [_pass(rid, component, "nextflow.preview.types = true present")]
-    return [_fail(rid, component, "Missing 'nextflow.preview.types = true'")]
+        return [_pass(rid, component, "nextflow.enable.types = true present")]
+    return [_fail(rid, component, "Missing 'nextflow.enable.types = true'")]
 
 
 def rule_m006(component: str, ctx: dict) -> list[LintResult]:

{bactopia-2.1.3 → bactopia-2.1.4}/bactopia/lint/rules/subworkflow_rules.py

@@ -35,11 +35,11 @@ def rule_s001(component: str, ctx: dict) -> list[LintResult]:
 
 
 def rule_s002(component: str, ctx: dict) -> list[LintResult]:
-    """nextflow.preview.types = true present."""
+    """nextflow.enable.types = true present."""
     rid = "S002"
     if ctx["structure"]["has_types_preview"]:
-        return [_pass(rid, component, "nextflow.preview.types = true present")]
-    return [_fail(rid, component, "Missing 'nextflow.preview.types = true'")]
+        return [_pass(rid, component, "nextflow.enable.types = true present")]
+    return [_fail(rid, component, "Missing 'nextflow.enable.types = true'")]
 
 
 def rule_s003(component: str, ctx: dict) -> list[LintResult]:

{bactopia-2.1.3 → bactopia-2.1.4}/bactopia/lint/rules/workflow_rules.py

@@ -26,11 +26,11 @@ def rule_w001(component: str, ctx: dict) -> list[LintResult]:
 
 
 def rule_w002(component: str, ctx: dict) -> list[LintResult]:
-    """nextflow.preview.types = true present."""
+    """nextflow.enable.types = true present."""
     rid = "W002"
     if ctx["structure"]["has_types_preview"]:
-        return [_pass(rid, component, "nextflow.preview.types = true present")]
-    return [_fail(rid, component, "Missing 'nextflow.preview.types = true'")]
+        return [_pass(rid, component, "nextflow.enable.types = true present")]
+    return [_fail(rid, component, "Missing 'nextflow.enable.types = true'")]
 
 
 def rule_w003(component: str, ctx: dict) -> list[LintResult]:

{bactopia-2.1.3 → bactopia-2.1.4}/bactopia/nf.py

@@ -723,8 +723,8 @@ def parse_main_nf_structure(main_nf: Path) -> dict:
 
     full_text = "".join(lines)
 
-    # Check for nextflow.preview.types = true
-    types_pattern = re.compile(r"nextflow\.preview\.types\s*=\s*true")
+    # Check for nextflow.enable.types = true (or legacy nextflow.preview.types)
+    types_pattern = re.compile(r"nextflow\.(?:enable|preview)\.types\s*=\s*true")
     result["has_types_preview"] = bool(types_pattern.search(full_text))
 
     # Extract process name (process UPPER_CASE {)
@@ -999,7 +999,7 @@ def parse_main_nf_structure(main_nf: Path) -> dict:
     )
 
     # Check for meta initialization (M018).
-    # Modules using nextflow.preview.types use: meta = record(id: ..., name: ..., ...)
+    # Modules using nextflow.enable.types use: meta = record(id: ..., name: ..., ...)
     # Legacy modules use: meta = [:] followed by meta.X = ... assignments.
     # The `(?<!_)` guard prevents matching `special_meta = record(...)`.
     result["has_meta_init"] = False

{bactopia-2.1.3 → bactopia-2.1.4}/bactopia/templates/nextflow/nextflow.config.j2

@@ -6,7 +6,7 @@ manifest {
     description = 'An extensive workflow for processing sequencing of bacterial genomes.'
     mainScript = 'main.nf'
     version = '4.0.0'
-    nextflowVersion = '>=25.04.6'
+    nextflowVersion = '>=26.04.0'
 }
 
 params {
@@ -93,7 +93,7 @@ dag {
 
 // Plugins
 plugins {
-    id 'nf-bactopia@2.0.0'
+    id 'nf-bactopia@2.1.0'
 }
 
 bactopia {

{bactopia-2.1.3 → bactopia-2.1.4}/bactopia/templates/scaffold/module/main.nf.j2

@@ -29,7 +29,7 @@
  * - `{{ output.name }}`: {{ output.description }}
 {% endfor %}
  */
-nextflow.preview.types = true
+nextflow.enable.types = true
 
 process {{ process_name }} {
     tag "${prefix}"

{bactopia-2.1.3 → bactopia-2.1.4}/bactopia/templates/scaffold/module/tests/nextflow.config.j2

@@ -1,5 +1,5 @@
 // Minimal config for module-level testing of {{ process_name }}
-nextflow.preview.types = true
+nextflow.enable.types = true
 nextflow.enable.strict = true
 
 params {

{bactopia-2.1.3 → bactopia-2.1.4}/bactopia/templates/scaffold/subworkflow/main.nf.j2

@@ -42,7 +42,7 @@
  * @output run_outputs
 {% endif %}
  */
-nextflow.preview.types = true
+nextflow.enable.types = true
 
 {% if has_csvtk %}
 {% set alias = process_name ~ " as " ~ process_name ~ "_MODULE" %}

{bactopia-2.1.3 → bactopia-2.1.4}/bactopia/templates/scaffold/subworkflow/tests/nextflow.config.j2

@@ -1,5 +1,5 @@
 // Minimal config for subworkflow-level testing of {{ process_name }}
-nextflow.preview.types = true
+nextflow.enable.types = true
 nextflow.enable.strict = true
 
 params {

{bactopia-2.1.3 → bactopia-2.1.4}/bactopia/templates/scaffold/workflow/main.nf.j2

@@ -36,7 +36,7 @@
  * @section Versions
  * @publish versions.yml               Software version information
  */
-nextflow.preview.types = true
+nextflow.enable.types = true
 
 params {
     rundir : String

{bactopia-2.1.3 → bactopia-2.1.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bactopia"
-version = "2.1.3"
+version = "2.1.4"
 description = "A Python package for working with Bactopia"
 authors = [
     "Robert A. Petit III <robbie.petit@gmail.com>",