## Issues Likely Already Fixed | Issue | Title | Evidence | |---|---|---| | #3985 | Support

val

in version topic channels |

main_nf.py:745

uses

(?:eval\|val)

regex | | #3710 | Update rich-click to 1.9 |

pyproject.toml

has

"rich-click==1.9.*"

| | #4066 | Subworkflows lint not comparing output channels |

subworkflows/lint/meta_yml.py:98-110

| | #4065 | Subworkflow meta.yml error with nested sbwf | Commit

eeeb73f9d

fixed state machine | | #4062 | Multi-line tuple interpreted as multiple inputs |

modules/lint/main_nf.py:127-133

| | #3941 | Linter drops trailing double quote in eval() topics | Commits

f0a7dad92

,

cda268c75

,

23d980bcb

| | #3901 |

modules lint --fix

produces mangled output | Commits

f0a7dad92

,

677915a2f

| | #3972 |

modules lint --fix

produces mangled output (follow-up) | Same fix as above | | #3889 |

task.process

without quotes crashes linting |

main_nf.py:744-746

fails gracefully | | #3844 | Subworkflow meta YML components mismatch |

meta_yml.py:132

guards with

if "components" in meta_yaml

| | #3927 |

files_unchanged

lint broken for custom pipelines |

files_unchanged.py:79-85

handles custom org | | #3794 | Schema error for integer with empty string default |

schema.py:204-207

checks empty string first | | #3772 |

modules lint

fails on patched modules |

main_nf.py:52-60

applies patch in reverse | | #2855 | Remove

tags.yml

from module template | No

tags.yml

in

nf_core/module-template/

| | #3979 | No

test_full

profile fails download CI |

download_pipeline.yml

only uses

test

profile | | #3573 |

.nf-core.yml

errors give unhelpful message |

utils.py:1462-1468

catches and reformats

ValidationError

| | #3763 | Outdated conda install / permission error |

pkg_resources

removed; user-environment issue | ## Partially Fixed / Needs Verification | Issue | Title | Notes | |---|---|---| | #4049 |

subworkflows lint <name> --local

doesn't work |

--local

alone works; named +

--local

combo may still clear list | | #3316 | Make

main

default for all nf-core repos |

tools

done; `modules`/`configs` still on `master`;

constants.py:6

still defaults to

"master"

| ## Still Open (confirmed not fixed) | Issue | Title | Evidence | |---|---|---| | #4054 |

--empty-template

not fully empty |

create.py:690-712

still pre-fills placeholders | | #3864 | Patch fails on binary/compressed files |

components_differ.py:79

opens in text mode | | #3708 |

modules patch

fails with Vim

.swp

files | No

.swp

filtering in

patch.py

| | #3703 | Switch

NF_CORE_MODULES_DEFAULT_BRANCH

to

main

|

constants.py:6

still

"master"

| | #3398 |

zenodo_release

in

.nf-core.yml

still warns |

readme.py:88

checks `zenodo_doi`; docs say

zenodo_release

| | #3685 | Migrate to

nf-core-utils

plugin | No

nf-core-utils

in pipeline template | | #3444 | Add

args

section in

meta.yml

| No

args

key in

module-template/meta.yml

| | #4031 |

nf-core update

all modules + subworkflows | No unified update-all command | | #2996 | Multiple

org_path

support |

utils.py:1392

is

str \| None

, not a list | | #4060 | Workflow handlers deprecated | `workflow.onComplete`/`onError` still in template | | #3270 | Phase out

when

directive | Module linting still requires

when:

|

I can start from the bottom!

i was also wondering that...

went through the last table (still open) adding tags (including

high-priority

for some 🙊). Some issues we should have an extra look to bring to the finish line, PRs are already created: • https://github.com/nf-core/tools/issues/3444 • https://github.com/nf-core/tools/issues/3708

updated lists with more issues