Merge pull request #44 from inutano/fix/nextflow-nxf-home

fix(nextflow): redirect NXF_HOME into run_dir to fix child container mount errors

Author: suecharo

sapporo/run.sh

@@ -60,6 +60,13 @@ function run_cwltool() {
 
 function run_nextflow() {
     local container="nextflow/nextflow:25.10.4"
+    # Store NXF_HOME inside the run_dir so pipeline assets (bin/ scripts, etc.)
+    # are on the host-mounted filesystem. Without this, Nextflow caches assets
+    # inside the container at /.nextflow/, which is not visible to the host.
+    # When child process containers are spawned, Nextflow tries to bind-mount
+    # those asset paths from the host, causing "mounts denied" errors.
+    local nxf_home="${run_dir}/nxf_home"
+    mkdir -p "${nxf_home}"
     # Write a Nextflow config that propagates DOCKER_API_VERSION into child containers.
     # This is required on Docker Desktop >= 4.x where the minimum supported API version
     # is 1.44, but the Docker client bundled in nextflow/nextflow images reports 1.32.
@@ -71,6 +78,8 @@ NFCFG
         -v /var/run/docker.sock:/var/run/docker.sock
         -e DOCKER_HOST=unix:///var/run/docker.sock
         -e DOCKER_API_VERSION=1.44
+        -e "NXF_HOME=${nxf_home}"
+        -e "NXF_ASSETS=${nxf_home}/assets"
         -v "${run_dir}:${run_dir}"
         "-w=${exe_dir}"
         "${container}"