WIP

Author: mtojek

.icons/nextflow.svg

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+---
+display_name: Nextflow
+description: A module that adds Nextflow to your Coder template.
+icon: ../../../../.icons/nextflow.svg
+verified: true
+tags: [nextflow, worfklow, 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/nextflow/coder"
+  version  = "0.9.0"
+  agent_id = coder_agent.example.id
+}
+```

registry/coder/modules/nextflow/README.md

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+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        = number
+  description = "Subdirectory for HTTP server reports, relative to the project path."
+  default     = "reports"
+}
+
+variable "checkout_demos" {
+  type        = bool
+  description = "Checkout demos?"
+  default     = false
+}
+
+variable "stub_run" {
+  type        = bool
+  description = "Execute a stub run?"
+  default     = false
+}
+
+variable "stub_run_command" {
+  type        = string
+  description = "Shell command to be executed during the stub run."
+  default     = "nextflow run . -stub-run"
+}
+
+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("${path.module}/run.sh", {
+    NEXTFLOW_VERSION : var.nextflow_version,
+    PROJECT_PATH : var.project_path,
+    HTTP_SERVER_PORT : var.http_server_port,
+    HTTP_SERVER_REPORTS_DIR : var.http_server_reports_dir,
+    CHECKOUT_DEMOS : var.checkout_demos,
+    STUB_RUN : var.stub_run,
+    STUB_RUN_COMMAND : var.stub_run_command,
+  })
+  run_on_start = true
+}
+
+resource "coder_app" "nextflow" {
+  agent_id     = var.agent_id
+  slug         = "nextflow-reports"
+  display_name = "Nextflow Reports"
+  url          = "http://localhost:${var.http_server_port}"
+  icon         = "/icon/nextflow.svg"
+  subdomain    = true
+  share        = var.share
+  order        = var.order
+  group        = var.group
+}