nf-core: init at 2.12.1

[edmundmiller]

Description of changes

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
  • sandbox = relaxed
  • sandbox = true
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 24.05 Release Notes (or backporting 23.05 and 23.11 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md.

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[zeuner]

Some thoughts.

[edmundmiller]

@zeuner Thanks! Addressed those issues.

[rollf]

Hey @edmundmiller
thanks for your work here. I tried to run nf-core create and run into this error:

I checked the code and this is likely simply due to the fact the the nix-based version will not have the "right" permissions in the store. But this code here assumes this.

Using the code snippet below (with pkgs.nf-core.overrideAttrs()), I was able to get nf-core create to run through. I don't think this is the way this should be done in the end but I nevertheless wanted to share this with you.

    postPatch = ''
      file=nf_core/create.py
      for line in "# Mirror file permissions" "template_stat = os.stat(template_fn_path)" "os.chmod(output_path, template_stat.st_mode)"; do
        sed -i "/$line/d" $file
      done
    '';

I'm not sure what a clean solution would be in the end. Probably not using sed, possibly a patch. But then also, I'm not sure whether it is problematic that the "true" file permissions are not available anymore.

For testing:

nf-core create --name workflow --author "" --description ""

[edmundmiller]

Thanks for testing that! Interesting solution as well.

I think that's a fine patch, maybe we can fix it on the nf-core side in future releases, and just check for permissions

[rollf]

@edmundmiller @zeuner I opened this PR to included nf-test. I would have added you as reviewers but I can't (I only seem to get suggestions for github handles starting with numbers and a).

[edmundmiller]

@edmundmiller @zeuner I opened this PR to included nf-test. I would have added you as reviewers but I can't (I only seem to get suggestions for github handles starting with numbers and a).

Awesome!

Aside: How'd you get it merged so fast? 😆 #286701 has been sitting there for months.

[nixos-discourse]

This pull request has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/prs-in-distress/3604/94

[doronbehar]

You should squash the commits in such a way that every package gets a single init commit, and the order of commits is such that Nixpkgs is able to evaluate correctly after every commit.

Other then that, looks good to me.

[rollf]

@edmundmiller Based on your PR, I currently use version 2.13.1 of nf-core and have updated my permission fix. Maybe you could integrate this? (Since this is a version bump, maybe a follow-up PR would be better ?). Compared to 2.12.1 the pipeline template has greatly changed.

  nf-core = pkgs-nf-core-2.nf-core.overrideAttrs (finalAttrs: previousAttrs: rec { # pkgs-nf-core-2 points to this PR
    version = "2.13.1";

    src = fetchFromGitHub {
      owner = "nf-core";
      repo = "tools";
      rev = version;
      hash = "sha256-Wda1dmc7FDgjXIuGdLFqlkuvMU+jUVzoEh2SDWGfOAY=";
    };

    postPatch = ''
      # https://github.com/nf-core/tools/blob/master/nf_core/create.py#L345-L347
      sed -i "/# Mirror file permissions/,+2d" nf_core/create.py
      # https://github.com/nf-core/tools/blob/9eac5e9b33a4b86a5228e950a8c8fd16765f4a85/nf_core/components/create.py#L285-L289
      sed -i "/# Mirror file permissions/,+4d" nf_core/components/create.py
    '';
  });