Strangely it is passing at the moment, it seems the install command
returns a passing exit code regardless of installing all modules.

- Addresses #2

This reverts commit 534da92.

tests: Add test case for cross-organization subwf

fix: Avoid duplicate downloads in nested subworkflows

* dev: (299 commits)
  Update nf_core/pipelines/create/utils.py
  [automated] Update CHANGELOG.md
  allow numbers in custom pipeline name
  [automated] Update CHANGELOG.md
  Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1
  Fixed linting
  Updated changelog
  Added process_high_memory to create/lint list
  update chagelog
  use pathlib instead of os.path
  Apply suggestions from code review
  add option to skip code linters
  Update gitpod/workspace-base Docker digest to f189a41
  Update pre-commit hook pre-commit/mirrors-mypy to v1.11.0
  [automated] Update CHANGELOG.md
  Update python:3.12-slim Docker digest to 740d94a
  Update .pre-commit-config.yaml
  Update nf_core/__main__.py
  Add default version
  Automatically add a default version in pipelines_create
  ...

* dev: (35 commits)
  don't remove creating a pipeline to test it 😶
  update textual snapshots
  update textual snapshots
  fix indentation
  Update nf_core/pipelines/create/create.py
  [automated] Update CHANGELOG.md
  [automated] Update CHANGELOG.md
  add option to exclude changelog from custom pipeline template
  add option to exclude codespaces from pipeline template
  remove multiqc images from the template docs
  and the same for subworkflows
  run tests also after pytest-migrate
  update textual snapshots
  add multiqc potion to test data
  update textual snapshots
  fix tests
  [automated] Update CHANGELOG.md
  add option to exclude multiqc from pipeline template
  rename regenerae-snapshots to update-textual-snapshots
  Apply suggestions from code review
  ...

This reverts commit 8e25587.

* dev: (35 commits)
  don't remove creating a pipeline to test it 😶
  update textual snapshots
  update textual snapshots
  fix indentation
  Update nf_core/pipelines/create/create.py
  [automated] Update CHANGELOG.md
  [automated] Update CHANGELOG.md
  add option to exclude changelog from custom pipeline template
  add option to exclude codespaces from pipeline template
  remove multiqc images from the template docs
  and the same for subworkflows
  run tests also after pytest-migrate
  update textual snapshots
  add multiqc potion to test data
  update textual snapshots
  fix tests
  [automated] Update CHANGELOG.md
  add option to exclude multiqc from pipeline template
  rename regenerae-snapshots to update-textual-snapshots
  Apply suggestions from code review
  ...

* fix/1927:

* feat/use-subwf:
  fix: Use sw_name in appends too
  fix: Use subworkflow name in recreate deps
  Revert "fix: Use name value in recreate deps"
  fix: Use name value in recreate deps
  fix: Change modules to subwfs
  refact: Support subwf dict in recreate deps
  refact: Rework logic to use subwfs as well

This reverts commit e9bf238.

refact: Add suggestions from 1st review round

* dev: (102 commits)
  [automated] Update CHANGELOG.md
  add templatefeatures.yml to python package
  fix typing
  Update nf_core/pipelines/create/utils.py
  set force to true when creating a pipeline from the app
  load feature yaml file with a utils function
  apply suggestions from code review by @mashehu
  reset lintconfigtype
  don't read from json on matrix creation
  try reading yaml keys with a list format
  update textual snapshots
  use template features yaml file to generate textual layout
  [automated] Update CHANGELOG.md
  handle template features with a yaml file
  update ruff
  fix tests
  fix refgenie tests
  add type hints to utils functions
  fix tests
  remove unnecessary string conversion
  ...

chore: Merge changes from dev

This reverts commit 0e83d9a.

…ge_get

Use the power of get to skip if tests

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>

refact: Change function structure to use dicts not lists

* upstream/dev: (45 commits)
  Apply suggestions from code review
  update textual snapshot
  add option to exclude adaptivecard and slackreport from pipeline template
  update pytest test_make_pipeline_schema
  [automated] Update CHANGELOG.md
  add option to exclude email from pipeline template
  update textual snapshots
  Update nf_core/pipelines/create/templatefeatures.yml
  [automated] Update CHANGELOG.md
  add option to exclude license from pipeline template
  [automated] Update CHANGELOG.md
  Update python:3.12-slim Docker digest to 59c7332
  [automated] Update CHANGELOG.md
  Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0
  Ran pre commit
  add matthias' suggestion woops
  Overwrite the verbose in ctx in case the user uses it
  Overwrite the verbose in ctx in case the user uses it
  Add a verbose click option
  run prettier on the pipeline output directory
  ...

* upstream/dev: (120 commits)
  markdown header
  add .gitignore to base required files
  update textual snapshots
  don't remove .gitignore when unselecting github
  update textual snapshots
  some more minimal template fixes
  udpate changelog
  handle cases where the directory path contains the name of the component
  switch to os.walk to support <3.10 versions of Python
  fix pipeline linting when skipping nf_schema
  update test to use template_features.yml and add missing files to a feature group
  rename templatefeatures.yml to template_features.yml
  update changelog
  fix linting
  add tests to ensure all files are part of a template customisation group
  add process cpus, memory and time to nextflow.config if we remove base.config
  update textual snapshots
  Revert "don't remove base.config when removing nf-core components"
  don't remove base.config when removing nf-core components
  apply review comments from @mashehu
  ...

* upstream/dev:
  Move if statements to top of YAML blocks
  Don't look for dev, look for not master
  Remove tests involving environment.yml with 'name'
  Remove name from conda enviroment.yml in module template
  Don't test conda `environment.yml` `name` attribute (which should no longer be there)
  Update CHANGELOG.md
  Add --update-all flag to remove defaults channels dependents
  add a tabix tabix test
  pre commit
  fix issue where tool and subtool have the same name
  udpate changelog
  run nf-core lint --release on PRs to master

refact: Add suggestions from second review

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>