Upd NextITS Dockerfile

image_development/Dockerfile_nextits_2

@@ -1,10 +1,31 @@
+ARG NEXTITS_VERSION=1.1.0
+ARG NEXTFLOW_VERSION=25.10.4
 
-# Stage 1 (Nextflow - minimal stage)
-FROM nextflow/nextflow:25.10.2 AS nextflow
+FROM vmikk/nextits:${NEXTITS_VERSION} AS main
 
-## Build stage 3 - Main
-FROM vmikk/nextits:1.1.0 AS main
+## Re-declare build args inside this stage so RUN can use them
+ARG NEXTITS_VERSION
+ARG NEXTFLOW_VERSION
 
-# Copy Nextflow binary from the Nextflow stage
-COPY --from=nextflow /usr/local/bin/nextflow /usr/local/bin/nextflow
+ENV NEXTITS_DIR=/opt/pipelines/NextITS
+ENV NXF_HOME=/opt/software/conda/bin
+# ENV PATH="${NXF_HOME}:${PATH}"
+
+USER root
+
+RUN set -eux; \
+    mkdir -p "${NXF_HOME}" "${NEXTITS_DIR}"; \
+    ## Install Nextflow into $NXF_HOME
+    NXF_VER="${NEXTFLOW_VERSION}" curl -s https://get.nextflow.io | bash ; \
+    mv nextflow "${NXF_HOME}/nextflow"; \
+    chmod 0755 "${NXF_HOME}/nextflow"; \
+    "${NXF_HOME}"/nextflow plugin install nf-schema@2.4.1; \
+    rm -rf ./.nextflow; \
+    ## Pull NextITS into $NEXTITS_DIR
+    git clone --depth 1 --branch "${NEXTITS_VERSION}" https://github.com/vmikk/NextITS "${NEXTITS_DIR}" ; \
+    rm -rf "${NEXTITS_DIR}/.git" ; \
+    ## Ensure the runtime user can access everything
+    chown -R nextits:nextits "${NXF_HOME}" "${NEXTITS_DIR}"
+
+USER nextits