run.sh

Author: mtojek

registry/coder/modules/nextflow/main.tf

@@ -38,12 +38,6 @@ variable "http_server_reports_dir" {
   default     = "reports"
 }
 
-variable "checkout_demos" {
-  type        = bool
-  description = "Checkout demos?"
-  default     = false
-}
-
 variable "stub_run" {
   type        = bool
   description = "Execute a stub run?"
@@ -52,8 +46,8 @@ variable "stub_run" {
 
 variable "stub_run_command" {
   type        = string
-  description = "Shell command to be executed during the stub run."
-  default     = "nextflow run . -stub-run"
+  description = "Nextflow command to be executed in the stub run."
+  default     = "run rnaseq-nf -with-report reports/report.html -with-trace reports/trace.txt -with-timeline reports/timeline.html -with-dag reports/flowchart.png"
 }
 
 variable "order" {
@@ -86,7 +80,6 @@ resource "coder_script" "nextflow" {
     PROJECT_PATH : var.project_path,
     HTTP_SERVER_PORT : var.http_server_port,
     HTTP_SERVER_REPORTS_DIR : var.http_server_reports_dir,
-    CHECKOUT_DEMOS : var.checkout_demos,
     STUB_RUN : var.stub_run,
     STUB_RUN_COMMAND : var.stub_run_command,
   })

registry/coder/modules/nextflow/run.sh

@@ -0,0 +1,53 @@
+#!/usr/bin/env sh
+
+set -eu
+
+BOLD='\033[0;1m'
+RESET='\033[0m'
+
+printf "$${BOLD}Starting Nextflow...$${RESET}\n"
+
+if ! command -v nextflow > /dev/null 2>&1; then
+    # Update system dependencies
+    sudo apt update
+    sudo apt install openjdk-18-jdk -y
+    sudo apt install salmon fastqc multiqc -y
+
+    # Install nextflow
+    export NXF_VER=${NEXTFLOW_VERSION}
+    curl -s https://get.nextflow.io | bash
+    sudo mv nextflow /usr/local/bin/
+    sudo chmod +x /usr/local/bin/nextflow
+
+    # Verify installation
+    tmp_verify=$$(mktemp -d coder-nextflow-XXXXXX)
+    nextflow run hello \
+        -with-report "$$tmp_verify/report.html" \
+        -with-trace "$$tmp_verify/trace.txt" \
+        -with-timeline "$$tmp_verify/timeline.html" \
+        -with-dag "$$tmp_verify/flowchart.png"
+    rm -f "$$tmp_verify"
+else
+    echo "Nextflow is already installed\n\n"
+fi
+
+if [ ! -z ${PROJECT_PATH} ]
+then
+    # Project is located at PROJECT_PATH
+    echo "Change directory: ${PROJECT_PATH}"
+    cd ${PROJECT_PATH}
+fi
+
+# Start a web server to preview reports
+mkdir -p ${HTTP_SERVER_REPORTS_DIR}
+python3 -m http.server --directory ${HTTP_SERVER_REPORTS_DIR} ${HTTP_SERVER_PORT}
+
+# Stub run?
+if [ "${STUB_RUN}" = "true" ]
+then
+    nextflow ${STUB_RUN_COMMAND} -stub-run
+fi
+
+printf "\n$${BOLD}Nextflow ${NEXTFLOW_VERSION} is ready. HTTP server is listening on port ${HTTP_SERVER_PORT}$${RESET}\n"
+
+