Add markdown output mode to lint command by ewels · Pull Request #6715 · nextflow-io/nextflow

ewels · 2026-01-13T07:59:14Z

I was building some automation around lint results and wanted to generate some nice markdown. I figured instead of writing that in my crappy Python script, I should do it upstream in Nextflow itself, then anyone can use it.

Add a new -o markdown option to the nextflow lint command
Generate markdown-formatted output for lint results with code snippets and caret highlighting
Update CLI documentation

PR details

The markdown output includes:

Header with title "Nextflow lint results"
Metadata: generation timestamp (ISO 8601), Nextflow version, summary counts
Errors section with :x: emoji (omitted if no errors)
Warnings section with :warning: emoji (omitted if no warnings)
Each entry shows filename:line:column, message, and code snippet with caret highlighting (^^^)

Errors and warnings are sorted by filename then by position.

Example output

# Nextflow lint results

- Generated: 2026-01-13T07:57:21.823435Z
- Nextflow version: 25.12.0-edge
- Summary: 2 errors

## :x: Errors

- Error: `/tmp/test_lint_a.nf:2:13`: `undefined_var` is not defined

    ```nextflow
        script: undefined_var
                ^^^^^^^^^^^^^
    ```

- Error: `/tmp/test_lint_b.nf:3:13`: `unknown` is not defined

    ```nextflow
        script: unknown
                ^^^^^^^
    ```

🤖 Generated with Claude Code

Example output:

nextflow lint -o markdown .

Nextflow lint results

Generated: 2026-01-13T08:03:30.620642Z
Nextflow version: 25.12.0-edge
Summary: 7 errors, 17 warnings

❌ Errors

Error: nextflow.config:293:28: manifest is not defined

\033[0;35m  nf-core/demo ${manifest.version}\033[0m
                           ^^^^^^^^

Error: nextflow.config:296:26: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                         ^^^^^^^^

Error: nextflow.config:296:69: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                    ^^^^^^^^

Error: nextflow.config:296:186: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                                                                         ^^^^^^^^

Error: nextflow.config:306:22: validation is not defined

        beforeText = validation.help.beforeText
                     ^^^^^^^^^^

Error: nextflow.config:307:21: validation is not defined

        afterText = validation.help.afterText
                    ^^^^^^^^^^

Error: nf-test.config:1:1: Config settings must be assigned with an equals sign (=)
```
config {
^
```

⚠️ Warnings

Warning: nextflow.config:296:129: Implicit closure parameter is deprecated, declare an explicit parameter instead

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                ^^

Warning: subworkflows/local/utils_nfcore_demo_pipeline/main.nf:31:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_demo_pipeline/main.nf:34:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_demo_pipeline/main.nf:38:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_demo_pipeline/main.nf:75:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```

Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:101:98: The use of Channel to access channel factories is deprecated -- use channel instead

    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
                                                                                                 ^^^^^^^

Warning: workflows/demo.nf:26:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/demo.nf:27:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/demo.nf:34:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
                                                                   ^^

Warning: workflows/demo.nf:44:9: Variable was declared but not used

        ch_trimmed  = SEQTK_TRIM.out.reads
        ^^^^^^^^^^

Warning: workflows/demo.nf:63:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/demo.nf:66:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/demo.nf:67:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/demo.nf:69:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/demo.nf:70:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```

Warning: workflows/demo.nf:74:27: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                          ^^^^^^^

Warning: workflows/demo.nf:80:45: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_methods_description                = Channel.value(
                                            ^^^^^^^

# Nextflow lint results

- Generated: 2026-01-13T08:03:30.620642Z
- Nextflow version: 25.12.0-edge
- Summary: 7 errors, 17 warnings

## :x: Errors

- Error: `nextflow.config:293:28`: `manifest` is not defined

    ```nextflow
    \033[0;35m  nf-core/demo ${manifest.version}\033[0m
                               ^^^^^^^^
    ```

- Error: `nextflow.config:296:26`: `manifest` is not defined

    ```nextflow
            afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                             ^^^^^^^^
    ```

- Error: `nextflow.config:296:69`: `manifest` is not defined

    ```nextflow
            afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                        ^^^^^^^^
    ```

- Error: `nextflow.config:296:186`: `manifest` is not defined

    ```nextflow
            afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                                                                             ^^^^^^^^
    ```

- Error: `nextflow.config:306:22`: `validation` is not defined

    ```nextflow
            beforeText = validation.help.beforeText
                         ^^^^^^^^^^
    ```

- Error: `nextflow.config:307:21`: `validation` is not defined

    ```nextflow
            afterText = validation.help.afterText
                        ^^^^^^^^^^
    ```

- Error: `nf-test.config:1:1`: Config settings must be assigned with an equals sign (`=`)

    ```nextflow
    config {
    ^
    ```


## :warning: Warnings

- Warning: `nextflow.config:296:129`: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ```nextflow
            afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                    ^^
    ```

- Warning: `subworkflows/local/utils_nfcore_demo_pipeline/main.nf:31:5`: Parameter was not used -- prefix with `_` to suppress warning

    ```nextflow
        monochrome_logs   // boolean: Do not use coloured log outputs
        ^^^^^^^^^^^^^^^
    ```

- Warning: `subworkflows/local/utils_nfcore_demo_pipeline/main.nf:34:5`: Parameter was not used -- prefix with `_` to suppress warning

    ```nextflow
        input             //  string: Path to input samplesheet
        ^^^^^
    ```

- Warning: `subworkflows/local/utils_nfcore_demo_pipeline/main.nf:38:19`: The use of `Channel` to access channel factories is deprecated -- use `channel` instead

    ```nextflow
        ch_versions = Channel.empty()
                      ^^^^^^^
    ```

- Warning: `subworkflows/local/utils_nfcore_demo_pipeline/main.nf:75:5`: The use of `Channel` to access channel factories is deprecated -- use `channel` instead

    ```nextflow
        Channel
        ^^^^^^^
    ```

- Warning: `subworkflows/nf-core/utils_nfcore_pipeline/main.nf:101:98`: The use of `Channel` to access channel factories is deprecated -- use `channel` instead

    ```nextflow
        return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
                                                                                                     ^^^^^^^
    ```

- Warning: `workflows/demo.nf:26:19`: The use of `Channel` to access channel factories is deprecated -- use `channel` instead

    ```nextflow
        ch_versions = Channel.empty()
                      ^^^^^^^
    ```

- Warning: `workflows/demo.nf:27:24`: The use of `Channel` to access channel factories is deprecated -- use `channel` instead

    ```nextflow
        ch_multiqc_files = Channel.empty()
                           ^^^^^^^
    ```

- Warning: `workflows/demo.nf:34:68`: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ```nextflow
        ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
                                                                       ^^
    ```

- Warning: `workflows/demo.nf:44:9`: Variable was declared but not used

    ```nextflow
            ch_trimmed  = SEQTK_TRIM.out.reads
            ^^^^^^^^^^
    ```

- Warning: `workflows/demo.nf:63:32`: The use of `Channel` to access channel factories is deprecated -- use `channel` instead

    ```nextflow
        ch_multiqc_config        = Channel.fromPath(
                                   ^^^^^^^
    ```

- Warning: `workflows/demo.nf:66:9`: The use of `Channel` to access channel factories is deprecated -- use `channel` instead

    ```nextflow
            Channel.fromPath(params.multiqc_config, checkIfExists: true) :
            ^^^^^^^
    ```

- Warning: `workflows/demo.nf:67:9`: The use of `Channel` to access channel factories is deprecated -- use `channel` instead

    ```nextflow
            Channel.empty()
            ^^^^^^^
    ```

- Warning: `workflows/demo.nf:69:9`: The use of `Channel` to access channel factories is deprecated -- use `channel` instead

    ```nextflow
            Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
            ^^^^^^^
    ```

- Warning: `workflows/demo.nf:70:9`: The use of `Channel` to access channel factories is deprecated -- use `channel` instead

    ```nextflow
            Channel.empty()
            ^^^^^^^
    ```

- Warning: `workflows/demo.nf:74:27`: The use of `Channel` to access channel factories is deprecated -- use `channel` instead

    ```nextflow
        ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                              ^^^^^^^
    ```

- Warning: `workflows/demo.nf:80:45`: The use of `Channel` to access channel factories is deprecated -- use `channel` instead

    ```nextflow
        ch_methods_description                = Channel.value(
                                                ^^^^^^^
    ```

Add a new `-o markdown` option to the `nextflow lint` command that generates markdown-formatted output for lint results. The markdown output includes: - Header with title "Nextflow lint results" - Metadata: generation timestamp (ISO 8601), Nextflow version, summary - Errors section with `:x:` emoji (omitted if no errors) - Warnings section with `:warning:` emoji (omitted if no warnings) - Each entry shows filename:line:column, message, and code snippet with caret highlighting Errors and warnings are sorted by filename then by position. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> Signed-off-by: Phil Ewels <phil.ewels@seqera.io>

netlify · 2026-01-13T07:59:20Z

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bentsherman · 2026-01-13T16:29:59Z

Tested it on nf-core/rnaseq and it works wonderfully. Well done Phil 👍

ewels requested a review from a team as a code owner January 13, 2026 07:59

ewels requested a review from bentsherman January 13, 2026 08:08

ewels mentioned this pull request Jan 13, 2026

Save markdown lint results nf-core/strict-syntax-health#3

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Merge branch 'master' into nextflow-lint-markdown

fddbccd

bentsherman approved these changes Jan 13, 2026

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bentsherman merged commit dad7c5d into master Jan 13, 2026
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bentsherman deleted the nextflow-lint-markdown branch January 13, 2026 16:38

pditommaso pushed a commit that referenced this pull request Jan 16, 2026

Add markdown output mode to lint command (#6715)

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Add markdown output mode to lint command#6715

Add markdown output mode to lint command#6715
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Example output

Nextflow lint results

❌ Errors

⚠️ Warnings

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