Bind clone engine inventory and launch to the installed Nextflow home

Author: MolBioFreak

modules/ngs/clone_validation.nf

@@ -77,14 +77,16 @@ process RunCloneValidation {
     def validator = shellQuote("${codeRoot}/scripts/validate_wf_clone_runtime.py")
     def lock = shellQuote(lockPath)
     def wfCloneSingularityCache = runtimeLock.containers.cache_dir
-    def wfCloneNxfHome = (params.wf_clone_nxf_home ?: System.getenv("NXF_HOME") ?: "${task.workDir}/.nextflow").toString()
+    def wfCloneNxfHome = (params.wf_clone_nxf_home ?: System.getenv("NXF_HOME") ?: "${System.getenv('HOME')}/.nextflow").toString()
     """
     set -euo pipefail
     export NXF_OFFLINE=true
     export NXF_DISABLE_CHECK_LATEST=true
     export NXF_DOCKER_ENABLED=false
     export NXF_SINGULARITY_CACHEDIR="${wfCloneSingularityCache}"
-    export NXF_HOME="${wfCloneNxfHome}"
+    export NXF_HOME=${shellQuote(wfCloneNxfHome)}
+    export NXF_VER=${shellQuote(runtimeLock.nextflow.version)}
+    export NXF_DIST="\${NXF_HOME}/framework"
     mkdir -p "\${NXF_HOME}"
 
     ${apiPython} ${validator} \

nextflow.config

@@ -1152,7 +1152,9 @@ params {
     // persistent shared cache explicitly; otherwise Nextflow stores remote
     // Singularity images under each task's wf_clone_work/singularity directory.
     wf_clone_singularity_cache = System.getenv('BMS_WF_CLONE_SINGULARITY_CACHE') ?: "${bmsContainerRootFallback}/singularity_cache"
-    wf_clone_nxf_home = System.getenv('BMS_WF_CLONE_NXF_HOME') ?: "${cacheRoot}/nextflow/wf-clone"
+    // Native compilation binds the installed engine home. Direct Nextflow use
+    // inherits its launcher home unless a clone-specific override is supplied.
+    wf_clone_nxf_home = System.getenv('BMS_WF_CLONE_NXF_HOME') ?: null
     wf_clone_runtime_lock = System.getenv('BMS_WF_CLONE_RUNTIME_LOCK') ?: "${params.code_root}/config/ngs/wf_clone_validation_v1.8.4.lock.json"
     wf_clone_basecaller_model = 'dna_r10.4.1_e8.2_400bps_hac@v6.0.0'
     wf_clone_sample = null

platform/api/native_components.py

@@ -1234,7 +1234,7 @@ def ngs_clone_runtime_dependencies(params):
     import os
     from pathlib import Path
     from component_runtime import SelectedDependency
-    from scripts.validate_wf_clone_runtime import resolve_lock_path, selected_images
+    from scripts.validate_wf_clone_runtime import resolve_lock_path, resolve_nextflow_home, selected_images
     root = Path(__file__).resolve().parents[2]
     lock_path = Path(params.get('wf_clone_runtime_lock') or os.environ.get('BMS_WF_CLONE_RUNTIME_LOCK') or
                      root / 'config/ngs/wf_clone_validation_v1.8.4.lock.json').resolve()
@@ -1257,7 +1257,7 @@ def add(kind, relative, path, sha256=None):
     add('runtime_data', prefix + '/compatibility.patch',
         resolve_lock_path(lock_path, lock['compatibility_patch']['path']),
         lock['compatibility_patch']['sha256'])
-    home = Path(params.get('wf_clone_nxf_home') or os.environ.get('NXF_HOME') or Path.home() / '.nextflow')
+    home = resolve_nextflow_home(params.get('wf_clone_nxf_home'))
     version = lock['nextflow']['version']
     jar = f'framework/{version}/nextflow-{version}-one.jar'
     add('runtime_data', prefix + '/nxf-home/' + jar, home / jar)

platform/api/services/nextflow.py

@@ -5676,6 +5676,12 @@ def resolve_antibody_validation_profile(default_profile: str) -> str:
         effective_profile = resolve_ont_workflow_alias(effective_profile)
         params = normalize_ont_launch_params(effective_profile, params)
         params['workflow_id'] = effective_profile
+        if (effective_profile == 'wf_clone_validation' or
+                (effective_profile == 'ont_construct_screening' and params.get('run_assembly') is True)):
+            from scripts.validate_wf_clone_runtime import resolve_nextflow_home
+            # Carry the installed engine selection into the plan and argv. The
+            # task must not invent a different cache after inventory selected it.
+            params['wf_clone_nxf_home'] = str(resolve_nextflow_home(params.get('wf_clone_nxf_home')))
     is_fastq_only_ont_command = (
         effective_profile == 'ont_fastq_qc'
         and str(params.get('ont_input_mode') or params.get('input_mode') or '').strip() == 'fastq'

platform/api/tests/test_workflow_cache_hygiene.py

@@ -23,7 +23,11 @@ def test_nested_wf_clone_has_shared_singularity_and_nxf_caches() -> None:
 
     assert "BMS_WF_CLONE_SINGULARITY_CACHE" in config_text
     assert 'wf_clone_singularity_cache = System.getenv(\'BMS_WF_CLONE_SINGULARITY_CACHE\') ?: "${bmsContainerRootFallback}/singularity_cache"' in config_text
-    assert 'wf_clone_nxf_home = System.getenv(\'BMS_WF_CLONE_NXF_HOME\') ?: "${cacheRoot}/nextflow/wf-clone"' in config_text
+    assert "wf_clone_nxf_home = System.getenv('BMS_WF_CLONE_NXF_HOME') ?: null" in config_text
+    assert '${cacheRoot}/nextflow/wf-clone' not in config_text
     assert 'apptainer.cacheDir = System.getenv(\'NXF_APPTAINER_CACHEDIR\') ?: ensureDir("${cacheRoot}/apptainer")' in config_text
     assert 'export NXF_SINGULARITY_CACHEDIR="${wfCloneSingularityCache}"' in module_text
-    assert 'export NXF_HOME="${wfCloneNxfHome}"' in module_text
+    assert 'export NXF_HOME=${shellQuote(wfCloneNxfHome)}' in module_text
+    assert 'export NXF_VER=${shellQuote(runtimeLock.nextflow.version)}' in module_text
+    assert 'export NXF_DIST="\\${NXF_HOME}/framework"' in module_text
+    assert '${task.workDir}/.nextflow' not in module_text

scripts/validate_wf_clone_runtime.py

@@ -83,6 +83,21 @@ def git(source: Path, *args: str) -> str:
     return result.stdout.strip()
 
 
+def resolve_nextflow_home(selected: str | Path | None = None) -> Path:
+    """Use the installed engine home, shared by inventory and native compilation.
+
+    Clone-specific/retained placement wins; otherwise inherit the managed
+    launcher home. Cache roots do not select an independently installed engine.
+    This resolves a path only: native launch retains its existing error behavior.
+    """
+    explicit = (selected or os.environ.get("BMS_WF_CLONE_NXF_HOME")
+                or os.environ.get("NXF_HOME") or os.environ.get("BMS_NEXTFLOW_HOME"))
+    if explicit:
+        return Path(explicit)
+    data = os.environ.get("BMS_DATA")
+    return Path(data) / "nextflow" if data else Path.home() / ".nextflow"
+
+
 def selected_images(lock: dict[str, Any], assembly_tool: str = "flye") -> list[dict[str, Any]]:
     """Only Canu is conditional; annotation and reporting always execute."""
     return [image for image in lock["containers"]["images"]