Merge branch 'master' into usearch/unoise3

.github/ISSUE_TEMPLATE/new_module.yml

@@ -27,6 +27,13 @@ body:
         - label: I have searched for existing issues
           required: true
 
+  - type: textarea
+    attributes:
+      label: Further Information
+      description: Is there a website, github repo or conda package? If yes enter the link here.
+    validations:
+      required: false
+
   - type: checkboxes
     attributes:
       label: Are you going to work on this?

.github/ISSUE_TEMPLATE/update_module.yml

@@ -0,0 +1,36 @@
+name: Update module
+description: Update a module in nf-core/modules
+title: "update module: TOOL/SUBTOOL"
+labels: update module
+body:
+  - type: checkboxes
+    attributes:
+      label: Is there an existing module for this?
+      description: This module already exists with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command
+      options:
+        - label: I have searched for the existing module
+          required: true
+
+  - type: checkboxes
+    attributes:
+      label: Is there an open PR for this?
+      description: There is no [open pull request](https://github.com/nf-core/modules/pulls) for this module
+      options:
+        - label: I have searched for existing PRs
+          required: true
+
+  - type: checkboxes
+    attributes:
+      label: Is there an open issue for this?
+      description: There is no [open issue](https://github.com/nf-core/modules/issues) for this module
+      options:
+        - label: I have searched for existing issues
+          required: true
+
+  - type: checkboxes
+    attributes:
+      label: Are you going to work on this?
+      description: If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
+      options:
+        - label: If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
+          required: false

.github/env-template.yml

@@ -1,4 +1,3 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults

.github/renovate.json5

@@ -20,7 +20,7 @@
         enabled: true,
     },
     customManagers: [
-        // TODO waiting on https://github.com/nf-core/modules/pull/4080
+    // TODO waiting on https://github.com/nf-core/modules/pull/4080
         // {
         //     customType: "regex",
         //     description: "Process Containers dependencies",
@@ -50,19 +50,19 @@
         //     ],
         //     datasourceTemplate: "pypi",
         // },
-    ],
+        ],
     packageRules: [
         {
             matchDatasources: ["docker"],
             registryUrls: ["quay.io"],
         },
         {
-            matchPackagePatterns: ["^nf-core/", "^seqera"],
             matchManagers: ["github-actions"],
             automerge: true,
             pinDigest: {
                 enabled: false,
             },
+            matchPackageNames: ["/^nf-core//", "/^seqera/"],
         },
         {
             matchManagers: ["github-actions"],
@@ -71,9 +71,9 @@
             schedule: ["before 9am"],
         },
         {
-            matchPackagePatterns: ["renovate-config-validator"],
             automerge: true,
             schedule: ["before 9am on Monday"],
+            matchPackageNames: ["/renovate-config-validator/"],
         },
     ],
 }

.github/scripts/license_message.py

@@ -12,15 +12,15 @@
 import re
 import secrets
 import sys
+from datetime import datetime as dt
 
 from cryptography.hazmat.primitives.ciphers.aead import AESGCM
-from datetime import datetime as dt
 
 MESSAGE_TIMEOUT = 60 * 60 * 24  # Messages are valid for 1 day
 NONCE_BYTES = 12
 
 
-class DecryptionTimeout(Exception):
+class DecryptionTimeoutError(Exception):
     # Decrypting a message that is too old
     pass
 
@@ -60,7 +60,7 @@ def decrypt_message(key, ciphertext, timeout=MESSAGE_TIMEOUT):
     msg_timestamp = int.from_bytes(msg_timestamp, byteorder="big")
     timestamp = calendar.timegm(dt.now().utctimetuple())
     if (timestamp - msg_timestamp) > timeout:
-        raise DecryptionTimeout("The message has an expired timeout")
+        raise DecryptionTimeoutError("The message has an expired timeout")
     return message.decode("utf-8")
 
 
@@ -82,9 +82,7 @@ def parse_args(argv=None):
 
     subparsers = parser.add_subparsers(help="Available sub-commands")
 
-    gen_parser = subparsers.add_parser(
-        "generate_key", help="Generate a random key string"
-    )
+    gen_parser = subparsers.add_parser("generate_key", help="Generate a random key string")
     gen_parser.set_defaults(func=handle_generate_key)
 
     encrypt_parser = subparsers.add_parser("encrypt", help="Encrypt a message")

.github/scripts/wave_singularity.py

@@ -0,0 +1,87 @@
+#!/usr/bin/env -S uv run
+# /// script
+# requires-python = ">=3.10"
+# dependencies = [
+#     "requests",
+#     "rich",
+# ]
+# ///
+
+import logging
+
+import requests
+import rich_click as click
+from rich.logging import RichHandler
+
+# Replace the basic logger setup with rich logging
+logging.basicConfig(
+    level=logging.INFO,
+    format="%(message)s",
+    handlers=[
+        RichHandler(
+            rich_tracebacks=True,
+            show_time=False,
+            markup=True,
+        )
+    ],
+)
+logger = logging.getLogger(__name__)
+click.rich_click.SHOW_ARGUMENTS = True
+
+
+@click.command()
+@click.option(
+    "--platform-pat",
+    envvar="SEQERA_ACCESS_TOKEN",
+    show_envvar=True,
+    help="Platform authentication token",
+)
+@click.argument("image_name")
+def main(image_name, platform_pat):
+    """Script to return a HTTPS Singularity image URL from Seqera Containers."""
+
+    if image_name.startswith("oras://"):
+        image_name = image_name.replace("oras://", "")
+
+    wave_api_url_base = "https://wave.seqera.io"
+    wave_api_url = f"{wave_api_url_base}/v1alpha1/inspect"
+    container_url_base = "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256"
+
+    request_data = {"containerImage": image_name}
+    if platform_pat:
+        request_data["toweraccesstoken"] = platform_pat
+    else:
+        logger.debug("'--platform-pat' / '$TOWER_ACCESS_TOKEN' not set, no auth to wave back end")
+
+    try:
+        logger.debug(f"Calling image inspect at {wave_api_url} for image url '{image_name}'")
+        response = requests.post(
+            url=wave_api_url,
+            json=request_data,
+            headers={"content-type": "application/json"},
+        )
+
+        data = response.json()
+        logger.debug(data)
+        layers = data.get("container", {}).get("manifest", {}).get("layers", [])
+        is_singularity = len(layers) == 1 and layers[0].get("mediaType", "").endswith(".sif")
+        logger.debug(layers)
+        if not is_singularity:
+            raise ValueError("Not a singularity image")
+        if "digest" not in layers[0]:
+            raise ValueError("no 'digest' in first layer found")
+
+        digest = layers[0]["digest"].replace("sha256:", "")
+        container_url = f"{container_url_base}/{digest[:2]}/{digest}/data"
+        print(container_url)
+
+    except requests.RequestException as exc:
+        raise ValueError(f"An error occurred while requesting {wave_api_url}\n {exc}")
+
+
+if __name__ == "__main__":
+    try:
+        main()
+    except ValueError as exc:
+        logger.error(f"[red]{exc}[/red]")
+        exit(1)

.github/workflows/fix-linting.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4
+      - uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php