From b5ba0192e5adf975686e2741d5388e07a5d66c24 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Mon, 18 Dec 2023 12:52:52 -0600
Subject: [PATCH] refactor: Make a Nextflow module

---
 hosts/framework/default.nix |  2 +-
 hosts/meshify/default.nix   |  2 +-
 modules/dev/java.nix        | 15 ---------------
 modules/dev/nextflow.nix    | 24 ++++++++++++++++++++++++
 4 files changed, 26 insertions(+), 17 deletions(-)
 delete mode 100644 modules/dev/java.nix
 create mode 100644 modules/dev/nextflow.nix

diff --git a/hosts/framework/default.nix b/hosts/framework/default.nix
index c1974452..5a7d15a4 100644
--- a/hosts/framework/default.nix
+++ b/hosts/framework/default.nix
@@ -55,8 +55,8 @@
     };
     dev = {
       cc.enable = true;
-      java.enable = true;
       julia.enable = true;
+      nextflow.enable = true;
       nixlang.enable = true;
       node.enable = true;
       node.enableGlobally = true;
diff --git a/hosts/meshify/default.nix b/hosts/meshify/default.nix
index 9e1b185e..ef728812 100644
--- a/hosts/meshify/default.nix
+++ b/hosts/meshify/default.nix
@@ -51,8 +51,8 @@
     };
     dev = {
       cc.enable = true;
-      java.enable = true;
       julia.enable = true;
+      nextflow.enable = true;
       nixlang.enable = true;
       node.enable = true;
       node.enableGlobally = true;
diff --git a/modules/dev/java.nix b/modules/dev/java.nix
deleted file mode 100644
index 5c9e7dae..00000000
--- a/modules/dev/java.nix
+++ /dev/null
@@ -1,15 +0,0 @@
-{
-  config,
-  options,
-  lib,
-  pkgs,
-  ...
-}:
-with lib;
-with lib.my; let
-  cfg = config.modules.dev.java;
-in {
-  options.modules.dev.java = {enable = mkBoolOpt false;};
-
-  config = mkIf cfg.enable {user.packages = with pkgs; [jdk17];};
-}
diff --git a/modules/dev/nextflow.nix b/modules/dev/nextflow.nix
new file mode 100644
index 00000000..b1231eb1
--- /dev/null
+++ b/modules/dev/nextflow.nix
@@ -0,0 +1,24 @@
+{
+  config,
+  options,
+  lib,
+  pkgs,
+  ...
+}:
+with lib;
+with lib.my; let
+  cfg = config.modules.dev.nextflow;
+in {
+  options.modules.dev.nextflow = {enable = mkBoolOpt false;};
+
+  config = mkIf cfg.enable {
+    user.packages = with pkgs; [
+      jdk17
+      my.nf-core
+    ];
+
+    environment.shellAliases = {
+      nf = "nextflow";
+    };
+  };
+}