PATH issue with Nextflow

flake.nix

{

  inputs = {
    nixpkgs.url = "nixpkgs/nixos-unstable";
  };

  description = "test";

  outputs = { self, nixpkgs }:
    let
      system = "x86_64-linux";
      pkgs = import nixpkgs { inherit system; };

      generateConfig = pkgs.runCommand "generateConfig" {
        propagatedBuildInputs = [ pkgs.nextflow pkgs.bwa ];
      } ''
                mkdir $out
                cat << EOF > $out/main.nf
                #!/usr/bin/env nextflow
                nextflow.enable.dsl=2

                process Bwa {
                    output:
                    file "test.txt"

                    """
                    bwa
                    """
                }
                workflow {
                    Bwa() | view
                }
                EOF
                '';
    in {
      packages.${system}.default = generateConfig;
      apps.${system}.default = {
        type = "app";
        name = "nextflowRun";
        program = "${pkgs.nextflow}/bin/nextflow";
      };
    };
}

this runs bwa when invoked as nix build && nix run . run result/main.nf:

{

  inputs = {
    nixpkgs.url = "nixpkgs/nixos-unstable";
  };

  description = "test";

  outputs = { self, nixpkgs }:
    let
      system = "x86_64-linux";
      pkgs = import nixpkgs { inherit system; };

      generateConfig = pkgs.runCommand "generateConfig" {
        propagatedBuildInputs = [ pkgs.nextflow pkgs.bwa ];
      } ''
        mkdir $out
        cat << EOF > $out/main.nf
        #!/usr/bin/env nextflow
        nextflow.enable.dsl=2
        process Bwa {
            output:
            file "test.txt"

            """
            export PATH=$PATH
            bwa
            """
        }
        workflow {
            Bwa() | view
        }
        EOF
      '';
    in {
      packages.${system}.default = generateConfig;
      apps.${system}.default = {
        type = "app";
        name = "nextflowRun";
        program = "${pkgs.nextflow}/bin/nextflow";
      };
    };
}

or this for a generic solution that makes stuff available to all calls of the default app

{

  inputs = {
    nixpkgs.url = "nixpkgs/nixos-unstable";
  };

  description = "test";

  outputs = { self, nixpkgs }:
    let
      system = "x86_64-linux";
      pkgs = import nixpkgs { inherit system; };

      generateConfig = pkgs.runCommand "generateConfig" {
        propagatedBuildInputs = [ pkgs.nextflow pkgs.bwa ];
      } ''
        mkdir $out
        cat << EOF > $out/main.nf
        #!/usr/bin/env nextflow
        nextflow.enable.dsl=2
        process Bwa {
            output:
            file "test.txt"

            """
            bwa
            """
        }
        workflow {
            Bwa() | view
        }
        EOF
      '';
    in {
      packages.${system}.default = generateConfig;
      apps.${system}.default = {
        type = "app";
        name = "nextflowRun";
        program = "${pkgs.writeShellScript "nextflow" ''
          export PATH="${pkgs.lib.makeBinPath generateConfig.propagatedBuildInputs}:$PATH"
          exec ${pkgs.nextflow}/bin/nextflow "$@"
        ''}";
      };
    };
}