Hi! This seems like a bug. I assume there is something wrong with my module (not sure what yet), but

nf-core modules lint

is not beign capable of showing the error and it's throwing an exception instead. Here is the PR: https://github.com/nf-core/modules/pull/9440

Hi everyone!! I'm trying to understand why I get fail lint on PR and linting works good on the actual code?? can anyone please take a look and see what you understand? https://github.com/nf-core/rnaseq/pull/1642/ Many thanks!

Can someone spot why lining fails here? https://github.com/nf-core/modules/actions/runs/21165056512/job/60867699106?pr=9678

Hi, can someone take a look, maybe you know how to fix meta.yml linting. specifically issue with ' Check the entry for topics. ' - how is that related? https://github.com/nf-core/modules/actions/runs/21399450470/job/61606251602?pr=9627

Hi, does anybody know why I get "'meta' map not emitted in output channel(s)" for a new

multiqc_sav

module? It is almost identical to

multiqc

, yet linting works fine on this module. Thank you! https://github.com/nf-core/modules/actions/runs/21643851630/job/62390686345?pr=9587

hey guys! I have some issue with

nf-core pipelines lint

, I am trying to get rid of the following warnings:

╭─ [!] 2 Module Test Warnings ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                 ╷                                ╷                                                                                                                                                                                                                     │
│ Module name     │ File path                      │ Test message                                                                                                                                                                                                        │
│╶────────────────┼────────────────────────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ quast           │ modules/nf-core/quast          │ New version available                                                                                                                                                                                               │
│ samtools/fastq  │ modules/nf-core/samtools/fastq │ New version available                                                                                                                                                                                               │
│                 ╵                                ╵                                                                                                                                                                                                                     │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

╭─ [!] 12 Subworkflow Test Warnings ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                   ╷                                                                                              ╷                                                                                                     │
│ Subworkflow name                                                  │ File path                                                                                    │ Test message                                                                                        │
│╶──────────────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline  │ subworkflows/local/utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline/main.nf  │ Included component 'completionSummary' not used in <http://main.nf|main.nf>                                          │
│ utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline  │ subworkflows/local/utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline/main.nf  │ Included component 'paramsSummaryMap' not used in <http://main.nf|main.nf>                                           │
│ utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline  │ subworkflows/local/utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline/main.nf  │ Included component 'UTILS_NEXTFLOW_PIPELINE' versions are not added in <http://main.nf|main.nf>                      │
│ utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline  │ subworkflows/local/utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline/main.nf  │ Included component 'UTILS_NFCORE_PIPELINE' versions are not added in <http://main.nf|main.nf>                        │
│ utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline  │ subworkflows/local/utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline/main.nf  │ Included component 'UTILS_NFSCHEMA_PLUGIN' versions are not added in <http://main.nf|main.nf>                        │
│ utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline  │ subworkflows/local/utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline/main.nf  │ Included component 'completionSummary' versions are not added in <http://main.nf|main.nf>                            │
│ utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline  │ subworkflows/local/utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline/main.nf  │ Included component 'paramsSummaryMap' versions are not added in <http://main.nf|main.nf>                             │
│ utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline  │ subworkflows/local/utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline/main.nf  │ Included component 'samplesheetToList' versions are not added in <http://main.nf|main.nf>                            │
│ utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline  │ subworkflows/local/utils_nfcore_879_wgs_microorganisms_taxonomy_resistance_pipeline/meta.yml │ Subworkflow meta.yml does not exist                                                                 │
│ utils_nextflow_pipeline                                           │ subworkflows/nf-core/utils_nextflow_pipeline                                                 │ New version available                                                                               │
│ utils_nfcore_pipeline                                             │ subworkflows/nf-core/utils_nfcore_pipeline                                                   │ New version available                                                                               │
│ utils_nfschema_plugin                                             │ subworkflows/nf-core/utils_nfschema_plugin                                                   │ New version available                                                                               │
│                                                                   ╵                                                                                              ╵                                                                                                     │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

How can I turn off any checks for modules and subworkflows. Do I add something like

modules: false

to

.nf-core.yml

?

pipelines lint

produces a warning for subworkflows

main_nf_version_emitted: Subworkflow does not emit software version

, do I assume correctly that similar to

main_nf_include_versions: Included component <modulename> versions are not added in <http://main.nf|main.nf>. Can be ignored if the module is using topic channels

I can ignore this if using topic channels?

And another question:

pipelines lint

tells me that my local subworkflows have issues. However, I am somehow unable to get

subworkflows lint

to also check my local subworkflows, i tried

nf-core subworkflows lint <subworkflowname>

,

nf-core subworkflows lint local/<subworkflowname>

and

nf-core subworkflows lint subworkflows/local/<subworkflowname>

Kinda related to linting, what code formater is recommender for nextflow code?

Prettier

?

There is

nextflow lint --format

but this has issues with some of the nf-core style and can cause some things to be changed in a way that isn't ideal. Personally I just format most of my nextflow code manually still at this point

Ah bummer, was hoping for something that I can set an forget

I just use the

nextflow lint --format

regardless of nf-core for that reason 😉. Supported in VSCode (if that's your IDE poison) with the Nextflow extension, with options to auto format on save etc

I have a meta.yml file where the topics break the linter. The file is attached, and running the linter with fix results in an error. This happens with 3.5.2 and the dev version (downloaded right now from Github). The error looks the same. Command I used nf-core modules lint rmats/prep --fix &> lint.log I guess it is indenting, but I don't know how to fix it.

Out of curiosity, I noticed that the pipelines all used to make use of

editorconfig

files and

eclint

to format

.nf

files and other files that prettier struggles with. But then this approach seems to have been abandonded. Why was this/is it considered bad practice to make use of this in a pipeline now?

What is the correct format for the contributors list in the manifest, I see some complains:

Could not parse `manifest.contributors` from nextflow.config. Expected a list of maps, for example: []. Normalised string passed to JSON parser was:
[{...},{...}]
JSON decoding error: Expecting ',' delimiter: line 1 column 3144 (char 3143)
No authors found in pipeline manifest. Proceeding without adding authors to the RO-Crate.

Weird thing I notice, the last entry, from the last contributo given back by tools is

"contribution":["contributor"}]

, while all other similar entries are

"contribution":["contributor"]}

. Notice how the

}

is weirdly placed. Any idea?

OK, I think I did something wrong on my side, I'll investigate deeper

What was the issue @Maxime Garcia? Running into the same problem 😞

it seems pre-commit linting is failing due to:

"errors": [
          {
              "filename": "subworkflows/nf-core/utils_nextflow_pipeline/main.nf",
              "startLine": 77,
              "startColumn": 25,
              "message": "`groovy.json.JsonGenerator.Options` is not defined"
          }
      ]

anyone else getting into the same issue?

Upon merging template 4.0.2, i keep getting the error:

files_unchanged: .github/PULL_REQUEST_TEMPLATE.md does not match the template

, when I run

nf-core pipelines lint --fix files_unchaged

locally or on devcontianer, the pull request template doens’t get updated. Anybody knows what’s wrong? https://github.com/nf-core/viralmetagenome/actions/runs/25849702727/job/75953014462?pr=289

quick question regarding the latest template update, the linter is expecting configuration files for different environments

conf/X

(conda, docker and singularity) yet mcmicro does not support conda. My first instinct was to delete the conda conf files but apparently the linter says no. What is the correct course of action for this? On the same note, regenerating conf files with

nextflow inspect

seems trivial for environments but not for architectures (amd64 vs arm64) what is the correct way to update them?

Still struggling with the static types in nf 26. The usual way to define igenomes reference using

fasta = getGenomeAttribute('fasta')

doesn't work anymore, and the only workaround I found is to define in

<http://main.nf|main.nf>

:

params.fasta: String  = getGenomeAttribute('fasta')
params.gtf:   String? = getGenomeAttribute('gtf')
...

However, the linting doesn't like it as it says that an invalid value for those params is passed (it expects a string, but nextflow.config doesn't declare them to avoid immutable issues at runtime). Have you faced the same issue? Do you have some solution other than adding these to the ignored params? Thanks!

Hello, I need help in this linting errors here https://github.com/nf-core/modules/actions/runs/27742205157/job/82071930502?pr=12027.

nf-core modules --fix lint

doesnt fix the errors. The environment.yml file is the one I use to create seqera containers, and it works for conda nicely. but linting doesnt like it..

Is the meta naming convention

'meta', 'meta2', 'meta3'

, a hard-rule? I'd like to stick to more descriptive names for https://github.com/nf-core/modules/pull/10027.

One more!

Error: Syntax errors in nf-test config file: java.net.NoRouteToHostException: No route to host

. Couldn't find any recent mentions of it on Slack. Source: https://github.com/nf-core/modules/actions/runs/28106565635/job/83222302993?pr=10027

hello i get this error :

─ [✗] 1 Module Test Failed ───────────────────────────────────────────────────╮
│                ╷                              ╷                              │
│ Module name    │ File path                    │ Test message                 │
│╶───────────────┼──────────────────────────────┼─────────────────────────────╴│
│ numorph/3dunet │ modules/nf-core/numorph/3du… │ singularity_tag: Unable to   │
│                │                              │ resolve singularity          │
│                │                              │ container                    │
│                ╵                              ╵                              │
╰──────────────────────────────────────────────────────────────────────────────╯

PR: https://github.com/nf-core/modules/pull/12130 i specify the container like this :

container "<http://quay.io/nf-core/numorph-3dunet:1.0.9|quay.io/nf-core/numorph-3dunet:1.0.9>"

all other tests pass. Not sure what I need to do to resolve this 😅 (from nf-core 4.0.3dev)

We used the bot to fix linting issue on this PR: https://github.com/nf-core/modules/pull/12188 But WAY too much things got commited: https://github.com/nf-core/modules/pull/12188/commits/0c431dc3d6b913c5dda56ad9b5bad49624a8a095

I added conda locks via

nf-core modules containers

to the BUSCO modules, but there is a dependency not available to ARM, so the ARM build failed. The linting throws error

No conda entries found for expected platform: linux/arm64

. Is there anything to do here, or just remove the containers sections from the meta for now? Build log: wave.seqera.io/view/builds/bd-aa7e45b61425a0b2_1 PR: github.com/nf-core/…/85757140634?pr=12272

Is there a way to skip linting of

meta.yml

files for local subworkflows only? I really cannot be bothered to write them and the linting warnings are ugly to me

Working on https://github.com/nf-core/demultiplex/pull/409 with tools 4.0.3. I updated modules via nf-core modules update which update the

conf/containers_*.config

files. I see some error on CI. I try the

--fix container_configs

options locally, but end up with a

KeyError: 'manifest.name'

error. Trying with 4.1.0, no error, but nothing gets updated on the config files side. Any idea, or should I go for a 4.1.0 TEMPLATE sync?

Given that

when

is deprecated by Nextflow (and yes I know some of us are not entirely satisfied with this - myself included) is there any thought given to switching off the

when_exist

lint check for modules by default?