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nf-core Strict Syntax Health Report

This repository tracks the health of nf-core pipelines, modules, and subworkflows with respect to Nextflow's strict syntax linting.

The Nextflow docs describes the differences from standard Nextflow syntax and includes many examples to help with migration and fixing errors. Strict syntax is backwards compatible with existing Nextflow code, but enforces stricter rules to catch common errors and improve code quality.

The goal is for all nf-core pipelines to run without errors using strict syntax.

Important

See the nf-core blog post for details on the migration timeline. Fixing all errors from nextflow lint will be a requirement by early spring 2026.

  • Last updated: 2026-03-11 00:23:04 UTC
  • Nextflow version: 26.02.0-edge

Pipelines

  • Total: 0 parse errors, 3098 errors, 8733 warnings across 131 pipelines
  • Zero errors: 34 pipelines (26.0%)
Errors Warnings
Errors Warnings
Pipeline Results (131 pipelines)
Pipeline Parse Error Errors Warnings Prints Help Lint Output Help Output
❌ oncoanalyser No 305 102 - View -
❌ airrflow No 150 135 - View -
❌ sarek No 143 577 - View -
❌ eager No 115 362 - View -
❌ hicar No 89 122 - View -
❌ genomeannotator No 85 148 - View -
❌ evexplorer No 75 53 - View -
❌ scnanoseq No 74 140 - View -
❌ diseasemodulediscovery No 69 80 - View -
❌ viralintegration No 66 13 - View -
❌ metatdenovo No 64 157 - View -
❌ cageseq No 62 69 - View -
❌ phageannotator No 59 98 - View -
❌ atacseq No 56 205 - View -
❌ variantcatalogue No 55 48 - View -
❌ readsimulator No 53 49 - View -
❌ metaboigniter No 52 123 - View -
❌ imcyto No 52 14 - View -
❌ spinningjenny No 50 9 - View -
❌ rnasplice No 49 190 - View -
❌ viralrecon No 49 99 - View -
❌ deepmutscan No 49 90 - View -
❌ chipseq No 47 181 - View -
❌ radseq No 45 42 - View -
❌ meerpipe No 44 84 - View -
❌ omicsgenetraitassociation No 44 30 - View -
❌ callingcards No 41 168 - View -
❌ lncpipe No 40 176 - View -
❌ genomeskim No 40 13 - View -
❌ circdna No 38 30 - View -
❌ marsseq No 37 64 - View -
❌ nanoseq No 36 43 - View -
❌ nascent No 34 162 - View -
❌ rarevariantburden No 33 22 - View -
❌ rnadnavar No 31 371 - View -
❌ multiplesequencealign No 31 158 - View -
❌ denovotranscript No 31 51 - View -
❌ genomeqc No 26 102 - View -
❌ magmap No 26 70 - View -
❌ abotyper No 26 64 - View -
❌ riboseq No 26 55 - View -
❌ scrnaseq No 22 94 - View -
❌ sammyseq No 21 148 - View -
❌ hic No 21 61 - View -
❌ mcmicro No 21 48 - View -
❌ datasync No 19 20 - View -
❌ mhcquant No 18 49 - View -
❌ cutandrun No 17 152 - View -
❌ phyloplace No 17 106 - View -
❌ bactmap No 17 31 - View -
❌ slamseq No 17 0 - View -
❌ pathogensurveillance No 16 437 - View -
❌ genomeassembler No 16 92 - View -
❌ diaproteomics No 16 0 - View -
❌ clipseq No 15 0 - View -
❌ mnaseseq No 15 0 - View -
❌ proteogenomicsdb No 15 0 - View -
❌ circrna No 14 157 - View -
❌ pangenome No 14 63 - View -
❌ tbanalyzer No 14 47 - View -
❌ rnafusion No 13 116 - View -
❌ detaxizer No 13 61 - View -
❌ crisprseq No 13 45 - View -
❌ sopa No 13 16 - View -
❌ differentialabundance No 12 47 - View -
❌ coproid No 12 46 - View -
❌ smrnaseq No 11 74 - View -
❌ metapep No 11 34 - View -
❌ hgtseq No 10 69 - View -
❌ deepmodeloptim No 10 49 - View -
❌ variantbenchmarking No 10 28 - View -
❌ tumourevo No 9 55 - View -
❌ pixelator No 9 36 - View -
❌ fastqrepair No 9 32 - View -
❌ proteinfold No 9 2 - View -
❌ hadge No 8 45 - View -
❌ pacsomatic No 7 115 - View -
❌ drugresponseeval No 7 29 - View -
❌ longraredisease No 6 121 - View -
❌ drop No 6 68 - View -
❌ tfactivity No 6 57 - View -
❌ cellpainting No 6 35 - View -
❌ pacvar No 6 29 - View -
❌ fastquorum No 6 28 - View -
❌ fetchngs No 6 25 - View -
❌ gwas No 6 16 - View -
❌ kmermaid No 6 16 - View -
❌ mitodetect No 6 16 - View -
❌ panoramaseq No 6 16 - View -
❌ troughgraph No 6 16 - View -
❌ viralmetagenome No 4 52 - View -
❌ methylarray No 4 19 - View -
❌ methylseq No 3 65 - View -
❌ reportho No 2 90 - View -
❌ dualrnaseq No 2 48 - View -
❌ pairgenomealign No 2 22 - View -
❌ raredisease No 1 0 - View -
❌ spatialxe No 0 98 No View View
✅ taxprofiler No 0 96 Yes View View
❌ methylong No 0 81 No View View
✅ funcscan No 0 73 Yes View View
✅ ampliseq No 0 66 Yes View View
✅ bacass No 0 44 Yes View View
❌ lsmquant No 0 43 No View View
❌ molkart No 0 42 No View View
✅ createtaxdb No 0 33 Yes View View
❌ isoseq No 0 31 No View View
✅ mag No 0 31 Yes View View
❌ references No 0 31 No View View
❌ stableexpression No 0 30 No View View
❌ ribomsqc No 0 27 No View View
❌ alleleexpression No 0 20 No View View
❌ scdownstream No 0 19 No View View
❌ createpanelrefs No 0 16 No View View
❌ hlatyping No 0 9 No View View
✅ rnaseq No 0 8 Yes View View
❌ seqsubmit No 0 6 No View View
❌ epitopeprediction No 0 5 No View View
❌ phaseimpute No 0 4 No View View
✅ genomicrelatedness No 0 3 Yes View View
✅ proteinfamilies No 0 3 Yes View View
✅ rangeland No 0 1 Yes View View
✅ seqinspector No 0 1 Yes View View
✅ bamtofastq No 0 0 Yes View View
✅ demo No 0 0 Yes View View
✅ demultiplex No 0 0 Yes View View
✅ nanostring No 0 0 Yes View View
✅ proteinannotator No 0 0 Yes View View
✅ rnavar No 0 0 Yes View View
✅ spatialvi No 0 0 Yes View View
❌ variantprioritization No 0 0 No View View

Modules

  • Total: 0 parse errors, 0 errors, 1 warnings across 1388 modules
  • Zero errors: 1388 modules (100.0%)
Errors Warnings
Errors Warnings
Module Results (0 modules with errors)
Module Parse Error Errors Warnings Lint Output

Modules with zero errors are not shown above (1388 modules). They may still have warnings. See the modules results directory for all lint outputs.

Subworkflows

  • Total: 0 parse errors, 0 errors, 0 warnings across 111 subworkflows
  • Zero errors: 111 subworkflows (100.0%)
Errors Warnings
Errors Warnings
Subworkflow Results (0 subworkflows with errors)
Subworkflow Parse Error Errors Warnings Lint Output

Subworkflows with zero errors are not shown above (111 subworkflows). They may still have warnings. See the subworkflows results directory for all lint outputs.

About

This report is generated daily by running nextflow lint on each nf-core pipeline, module, and subworkflow. The linting checks for strict syntax compliance in Nextflow DSL2 code.

  • Parse errors indicate items where nextflow lint could not run at all, typically due to syntax errors that prevent Nextflow from parsing the code
  • Errors indicate syntax issues that will cause problems in future Nextflow versions
  • Warnings indicate deprecated patterns that should be updated, but having warnings is fine (though it's nice to fix those as well if possible)
  • Prints Help (pipelines only) tests whether the pipeline can print its help message using the v2 syntax parser (NXF_SYNTAX_PARSER=v2 nextflow run . --help). This test only runs for pipelines with zero lint errors.

Running Locally

You can run nextflow lint on your own pipeline to check for strict syntax issues:

nextflow lint .

Note: Until this fix is included in a Nextflow edge release, you may need to exclude nf-test files manually:

nextflow lint . -exclude ".git,.nf-test,nf-test.config"

See the strict syntax documentation for more information about the rules being checked.

Getting Help

If you need help fixing strict syntax errors in your pipeline, the Nextflow community forum is a great place to ask questions.

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Track Nextflow strict syntax linting health across nf-core pipelines

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