Update nf-core to 3.0.0 (#51249)

* Update nf-core to 3.0.0

* update deps

* try commenting out pdiff for now

* add git back to run section

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

recipes/nf-core/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "nf-core" %}
-{% set version = "2.14.1" %}
-{% set sha256 = "35bd8d73ecca4eb87443fada31bc7b2562429de3a4bfbf7261db348d14bf54bb" %}
+{% set version = "3.0.0" %}
+{% set sha256 = "ab67b23840104f7f4125b13519ced9c8021494c03d2eba3f9af6bb3176588846" %}
 
 package:
   name: {{ name|lower }}
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: python
-  number: 1
+  number: 0
   script: "touch requirements.txt && {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   entry_points:
     - nf-core=nf_core.__main__:run_nf_core
@@ -23,33 +23,34 @@ requirements:
   host:
     - python >=3.8
     - pip
-    - twine
   run:
     - python >=3.8
     - click
     - filetype
-    - galaxy-tool-util
     - git
     - gitpython
+    - pygithub
     - jinja2
-    - jsonschema >=3.0
+    - jsonschema >=4.0
     - markdown >=3.3
     - packaging
     - pillow
+    #- pdiff
     - pre-commit
-    - prompt_toolkit >=3.0.3
-    - pytest >=7.0.0
-    - pytest-workflow >=1.6.0
+    - prompt_toolkit >=3.0.36
+    - pydantic >=2.2.1
     - pyyaml
-    - questionary >=1.8.0
+    - questionary >=2.0.1
     - refgenie
     - requests
     - requests-cache
     - rich >=13.3.1
-    - rich-click >=1.6.1
+    - rich-click ==1.8.*
+    - ruamel.yaml
     - tabulate
+    - textual ==0.71.0
     - trogon
-    - nextflow >=23.04.0
+    - nextflow >=24.04.4
     - nf-test
 
 test:
@@ -59,13 +60,18 @@ test:
     - nf-test version
 
 about:
-  home: http://nf-co.re/
+  home: "https://nf-co.re"
   license: MIT
   license_family: MIT
+  license_file: LICENSE
   summary: 'Python package with helper tools for the nf-core community.'
+  dev_url: "https://github.com/nf-core/tools"
+  doc_url: "https://nf-co.re"
 
 extra:
   container:
     # click requires a unicode locale when used with Python 3
     # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly
-    extended-base: true
+    extended-base: True
+  identifiers:
+    - doi:10.1038/s41587-020-0439-x