add: nextflow module (#416)

Author: mtojek

.icons/nextflow.svg

@@ -0,0 +1,22 @@
+---
+display_name: Nextflow
+description: A module that adds Nextflow to your Coder template.
+icon: ../../../../.icons/nextflow.svg
+verified: true
+tags: [nextflow, workflow, hpc, bioinformatics]
+---
+
+# Nextflow
+
+A module that adds Nextflow to your Coder template.
+
+![Nextflow](../../.images/nextflow.png)
+
+```tf
+module "nextflow" {
+  count    = data.coder_workspace.me.start_count
+  source   = "registry.coder.com/coder-labs/nextflow/coder"
+  version  = "0.9.0"
+  agent_id = coder_agent.example.id
+}
+```

registry/coder-labs/modules/nextflow/README.md

@@ -0,0 +1,106 @@
+terraform {
+  required_version = ">= 1.0"
+
+  required_providers {
+    coder = {
+      source  = "coder/coder"
+      version = ">= 2.5"
+    }
+  }
+}
+
+# Add required variables for your modules and remove any unneeded variables
+variable "agent_id" {
+  type        = string
+  description = "The ID of a Coder agent."
+}
+
+variable "nextflow_version" {
+  type        = string
+  description = "Nextflow version"
+  default     = "25.04.7"
+}
+
+variable "project_path" {
+  type        = string
+  description = "The path to Nextflow project, it will be mounted in the container."
+}
+
+variable "http_server_port" {
+  type        = number
+  description = "The port to run HTTP server on."
+  default     = 9876
+}
+
+variable "http_server_reports_dir" {
+  type        = string
+  description = "Subdirectory for HTTP server reports, relative to the project path."
+  default     = "reports"
+}
+
+variable "http_server_log_path" {
+  type        = string
+  description = "HTTP server logs"
+  default     = "/tmp/nextflow_reports.log"
+}
+
+variable "stub_run" {
+  type        = bool
+  description = "Execute a stub run?"
+  default     = false
+}
+
+variable "stub_run_command" {
+  type        = string
+  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" {
+  type        = number
+  description = "The order determines the position of app in the UI presentation. The lowest order is shown first and apps with equal order are sorted by name (ascending order)."
+  default     = null
+}
+
+variable "share" {
+  type    = string
+  default = "owner"
+  validation {
+    condition     = var.share == "owner" || var.share == "authenticated" || var.share == "public"
+    error_message = "Incorrect value. Please set either 'owner', 'authenticated', or 'public'."
+  }
+}
+
+variable "group" {
+  type        = string
+  description = "The name of a group that this app belongs to."
+  default     = null
+}
+
+resource "coder_script" "nextflow" {
+  agent_id     = var.agent_id
+  display_name = "nextflow"
+  icon         = "/icon/nextflow.svg"
+  script = templatefile("${path.module}/run.sh", {
+    NEXTFLOW_VERSION : var.nextflow_version,
+    PROJECT_PATH : var.project_path,
+    HTTP_SERVER_PORT : var.http_server_port,
+    HTTP_SERVER_REPORTS_DIR : var.http_server_reports_dir,
+    HTTP_SERVER_LOG_PATH : var.http_server_log_path,
+    STUB_RUN : var.stub_run,
+    STUB_RUN_COMMAND : var.stub_run_command,
+  })
+  run_on_start = true
+}
+
+resource "coder_app" "nextflow" {
+  agent_id     = var.agent_id
+  slug         = "nextflow-reports"
+  display_name = "Nextflow Reports"
+  url          = "http://localhost:${var.http_server_port}"
+  icon         = "/icon/nextflow.svg"
+  subdomain    = true
+  share        = var.share
+  order        = var.order
+  group        = var.group
+}

registry/coder-labs/modules/nextflow/main.tf

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+#!/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-21-jdk graphviz 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 -r "$${tmp_verify}"
+else
+  echo "Nextflow is already installed\n\n"
+fi
+
+if [ ! -z ${PROJECT_PATH} ]; then
+  # Project is located at PROJECT_PATH
+  echo "Change directory: ${PROJECT_PATH}"
+  cd ${PROJECT_PATH}
+fi
+
+# Start a web server to preview reports
+mkdir -p ${HTTP_SERVER_REPORTS_DIR}
+echo "Starting HTTP server in background, check logs: ${HTTP_SERVER_LOG_PATH}"
+python3 -m http.server --directory ${HTTP_SERVER_REPORTS_DIR} ${HTTP_SERVER_PORT} > "${HTTP_SERVER_LOG_PATH}" 2>&1 &
+
+# Stub run?
+if [ "${STUB_RUN}" = "true" ]; then
+  nextflow ${STUB_RUN_COMMAND} -stub-run
+fi
+
+printf "\n$${BOLD}Nextflow ${NEXTFLOW_VERSION} is ready. HTTP server is listening on port ${HTTP_SERVER_PORT}$${RESET}\n"