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‎README.md‎

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> See the [nf-core blog post](https://nf-co.re/blog/2025/nextflow_syntax_nf-core_roadmap) for details on the migration timeline.
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> **Fixing all errors from `nextflow lint` will be a requirement by early spring 2026.**
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- **Last updated:** 2026-02-26 00:22:29 UTC
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- **Last updated:** 2026-02-27 00:28:04 UTC
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- **Nextflow version:** 26.01.1-edge
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## Pipelines
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- **Total:** 0 parse errors, 3192 errors, 9203 warnings across 132 pipelines
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- **Total:** 0 parse errors, 3194 errors, 9204 warnings across 132 pipelines
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- **Zero errors:** 32 pipelines (24.2%)
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| Errors | Warnings |
@@ -51,7 +51,7 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
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| :x: [rnasplice](https://github.com/nf-core/rnasplice) | No | 49 | 190 | - | [View](lint_results/pipeline-results/rnasplice_lint.md) | - |
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| :x: [viralrecon](https://github.com/nf-core/viralrecon) | No | 49 | 99 | - | [View](lint_results/pipeline-results/viralrecon_lint.md) | - |
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| :x: [chipseq](https://github.com/nf-core/chipseq) | No | 47 | 181 | - | [View](lint_results/pipeline-results/chipseq_lint.md) | - |
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| :x: [riboseq](https://github.com/nf-core/riboseq) | No | 45 | 146 | - | [View](lint_results/pipeline-results/riboseq_lint.md) | - |
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| :x: [riboseq](https://github.com/nf-core/riboseq) | No | 46 | 143 | - | [View](lint_results/pipeline-results/riboseq_lint.md) | - |
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| :x: [radseq](https://github.com/nf-core/radseq) | No | 45 | 42 | - | [View](lint_results/pipeline-results/radseq_lint.md) | - |
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| :x: [meerpipe](https://github.com/nf-core/meerpipe) | No | 44 | 84 | - | [View](lint_results/pipeline-results/meerpipe_lint.md) | - |
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| :x: [omicsgenetraitassociation](https://github.com/nf-core/omicsgenetraitassociation) | No | 44 | 30 | - | [View](lint_results/pipeline-results/omicsgenetraitassociation_lint.md) | - |
@@ -97,12 +97,12 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
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| :x: [pacvar](https://github.com/nf-core/pacvar) | No | 12 | 54 | - | [View](lint_results/pipeline-results/pacvar_lint.md) | - |
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| :x: [coproid](https://github.com/nf-core/coproid) | No | 12 | 46 | - | [View](lint_results/pipeline-results/coproid_lint.md) | - |
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| :x: [smrnaseq](https://github.com/nf-core/smrnaseq) | No | 11 | 74 | - | [View](lint_results/pipeline-results/smrnaseq_lint.md) | - |
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| :x: [pixelator](https://github.com/nf-core/pixelator) | No | 11 | 36 | - | [View](lint_results/pipeline-results/pixelator_lint.md) | - |
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| :x: [metapep](https://github.com/nf-core/metapep) | No | 11 | 34 | - | [View](lint_results/pipeline-results/metapep_lint.md) | - |
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| :x: [variantbenchmarking](https://github.com/nf-core/variantbenchmarking) | No | 10 | 74 | - | [View](lint_results/pipeline-results/variantbenchmarking_lint.md) | - |
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| :x: [hgtseq](https://github.com/nf-core/hgtseq) | No | 10 | 69 | - | [View](lint_results/pipeline-results/hgtseq_lint.md) | - |
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| :x: [variantbenchmarking](https://github.com/nf-core/variantbenchmarking) | No | 10 | 69 | - | [View](lint_results/pipeline-results/variantbenchmarking_lint.md) | - |
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| :x: [mhcquant](https://github.com/nf-core/mhcquant) | No | 10 | 63 | - | [View](lint_results/pipeline-results/mhcquant_lint.md) | - |
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| :x: [deepmodeloptim](https://github.com/nf-core/deepmodeloptim) | No | 10 | 49 | - | [View](lint_results/pipeline-results/deepmodeloptim_lint.md) | - |
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| :x: [pixelator](https://github.com/nf-core/pixelator) | No | 10 | 38 | - | [View](lint_results/pipeline-results/pixelator_lint.md) | - |
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| :x: [tumourevo](https://github.com/nf-core/tumourevo) | No | 9 | 55 | - | [View](lint_results/pipeline-results/tumourevo_lint.md) | - |
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| :x: [fastqrepair](https://github.com/nf-core/fastqrepair) | No | 9 | 32 | - | [View](lint_results/pipeline-results/fastqrepair_lint.md) | - |
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| :x: [hadge](https://github.com/nf-core/hadge) | No | 8 | 45 | - | [View](lint_results/pipeline-results/hadge_lint.md) | - |
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| :x: [dualrnaseq](https://github.com/nf-core/dualrnaseq) | No | 2 | 48 | - | [View](lint_results/pipeline-results/dualrnaseq_lint.md) | - |
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| :x: [pairgenomealign](https://github.com/nf-core/pairgenomealign) | No | 2 | 22 | - | [View](lint_results/pipeline-results/pairgenomealign_lint.md) | - |
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| :x: [seqsubmit](https://github.com/nf-core/seqsubmit) | No | 1 | 32 | - | [View](lint_results/pipeline-results/seqsubmit_lint.md) | - |
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| :x: [phaseimpute](https://github.com/nf-core/phaseimpute) | No | 1 | 15 | - | [View](lint_results/pipeline-results/phaseimpute_lint.md) | - |
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| :x: [phaseimpute](https://github.com/nf-core/phaseimpute) | No | 1 | 16 | - | [View](lint_results/pipeline-results/phaseimpute_lint.md) | - |
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| :white_check_mark: [taxprofiler](https://github.com/nf-core/taxprofiler) | No | 0 | 112 | Yes | [View](lint_results/pipeline-results/taxprofiler_lint.md) | [View](lint_results/prints-help-results/taxprofiler_help.txt) |
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| :x: [spatialxe](https://github.com/nf-core/spatialxe) | No | 0 | 98 | No | [View](lint_results/pipeline-results/spatialxe_lint.md) | [View](lint_results/prints-help-results/spatialxe_help.txt) |
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| :x: [methylong](https://github.com/nf-core/methylong) | No | 0 | 81 | No | [View](lint_results/pipeline-results/methylong_lint.md) | [View](lint_results/prints-help-results/methylong_help.txt) |
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| :x: [createpanelrefs](https://github.com/nf-core/createpanelrefs) | No | 0 | 16 | No | [View](lint_results/pipeline-results/createpanelrefs_lint.md) | [View](lint_results/prints-help-results/createpanelrefs_help.txt) |
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| :x: [hlatyping](https://github.com/nf-core/hlatyping) | No | 0 | 9 | No | [View](lint_results/pipeline-results/hlatyping_lint.md) | [View](lint_results/prints-help-results/hlatyping_help.txt) |
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| :x: [epitopeprediction](https://github.com/nf-core/epitopeprediction) | No | 0 | 5 | No | [View](lint_results/pipeline-results/epitopeprediction_lint.md) | [View](lint_results/prints-help-results/epitopeprediction_help.txt) |
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| :white_check_mark: [rnaseq](https://github.com/nf-core/rnaseq) | No | 0 | 5 | Yes | [View](lint_results/pipeline-results/rnaseq_lint.md) | [View](lint_results/prints-help-results/rnaseq_help.txt) |
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| :x: [rnaseq](https://github.com/nf-core/rnaseq) | No | 0 | 5 | No | [View](lint_results/pipeline-results/rnaseq_lint.md) | [View](lint_results/prints-help-results/rnaseq_help.txt) |
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| :white_check_mark: [proteinfold](https://github.com/nf-core/proteinfold) | No | 0 | 2 | Yes | [View](lint_results/pipeline-results/proteinfold_lint.md) | [View](lint_results/prints-help-results/proteinfold_help.txt) |
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| :white_check_mark: [rangeland](https://github.com/nf-core/rangeland) | No | 0 | 1 | Yes | [View](lint_results/pipeline-results/rangeland_lint.md) | [View](lint_results/prints-help-results/rangeland_help.txt) |
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| :white_check_mark: [bamtofastq](https://github.com/nf-core/bamtofastq) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/bamtofastq_lint.md) | [View](lint_results/prints-help-results/bamtofastq_help.txt) |
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## Modules
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- **Total:** 0 parse errors, 0 errors, 0 warnings across 1381 modules
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- **Zero errors:** 1381 modules (100.0%)
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- **Total:** 0 parse errors, 0 errors, 0 warnings across 1382 modules
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- **Zero errors:** 1382 modules (100.0%)
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| Errors | Warnings |
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| :----------------------------------------: | :--------------------------------------------: |
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| Module | Parse Error | Errors | Warnings | Lint Output |
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| ------ | :---------: | -----: | -------: | :---------: |
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_Modules with zero errors are not shown above (1381 modules). They may still have warnings. See the [modules results directory](lint_results/module-results/) for all lint outputs._
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_Modules with zero errors are not shown above (1382 modules). They may still have warnings. See the [modules results directory](lint_results/module-results/) for all lint outputs._
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</details>
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‎lint_results/module-results/abricate_run_lint.md‎

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# Nextflow lint results
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- Generated: 2026-02-26T00:21:45.490836+00:00
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- Generated: 2026-02-27T00:27:28.426068+00:00
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- Nextflow version: 26.01.1-edge
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- Summary: No issues found

‎lint_results/module-results/abricate_summary_lint.md‎

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# Nextflow lint results
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- Generated: 2026-02-26T00:21:45.491001+00:00
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- Generated: 2026-02-27T00:27:28.426233+00:00
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- Nextflow version: 26.01.1-edge
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- Summary: No issues found

‎lint_results/module-results/abritamr_run_lint.md‎

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# Nextflow lint results
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- Generated: 2026-02-26T00:21:45.491142+00:00
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- Generated: 2026-02-27T00:27:28.426360+00:00
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- Nextflow version: 26.01.1-edge
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- Summary: No issues found

‎lint_results/module-results/affy_justrma_lint.md‎

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# Nextflow lint results
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- Generated: 2026-02-26T00:21:45.491299+00:00
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- Generated: 2026-02-27T00:27:28.426468+00:00
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- Nextflow version: 26.01.1-edge
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- Summary: No issues found

‎lint_results/module-results/agat_convertbed2gff_lint.md‎

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# Nextflow lint results
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- Generated: 2026-02-26T00:21:45.491437+00:00
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- Generated: 2026-02-27T00:27:28.426588+00:00
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- Nextflow version: 26.01.1-edge
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- Summary: No issues found

‎lint_results/module-results/agat_convertgff2bed_lint.md‎

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# Nextflow lint results
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- Generated: 2026-02-26T00:21:45.491570+00:00
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- Generated: 2026-02-27T00:27:28.426688+00:00
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- Nextflow version: 26.01.1-edge
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- Summary: No issues found

‎lint_results/module-results/agat_convertspgff2gtf_lint.md‎

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# Nextflow lint results
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- Generated: 2026-02-26T00:21:45.491702+00:00
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- Generated: 2026-02-27T00:27:28.426807+00:00
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- Nextflow version: 26.01.1-edge
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- Summary: No issues found

‎lint_results/module-results/agat_convertspgff2tsv_lint.md‎

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# Nextflow lint results
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- Generated: 2026-02-26T00:21:45.491834+00:00
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- Generated: 2026-02-27T00:27:28.426917+00:00
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- Nextflow version: 26.01.1-edge
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- Summary: No issues found

‎lint_results/module-results/agat_convertspgxf2gxf_lint.md‎

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# Nextflow lint results
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- Generated: 2026-02-26T00:21:45.491967+00:00
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- Generated: 2026-02-27T00:27:28.427016+00:00
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- Nextflow version: 26.01.1-edge
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- Summary: No issues found

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