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: 2026-03-26 00:28:43 UTC
• Nextflow version: 26.03.0-edge

Pipelines

• Total: 0 parse errors, 2880 errors, 8165 warnings across 133 pipelines
• Zero errors: 44 pipelines (33.1%)

Errors	Warnings

Pipeline Results (133 pipelines)

Pipeline	Parse Error	Errors	Warnings	Prints Help	Lint Output	Help Output
❌ oncoanalyser	No	305	102	-	View	-
❌ airrflow	No	188	135	-	View	-
❌ sarek	No	119	549	-	View	-
❌ eager	No	115	362	-	View	-
❌ hicar	No	89	122	-	View	-
❌ genomeannotator	No	85	148	-	View	-
❌ evexplorer	No	75	53	-	View	-
❌ scnanoseq	No	73	140	-	View	-
❌ diseasemodulediscovery	No	69	80	-	View	-
❌ viralintegration	No	66	13	-	View	-
❌ phageannotator	No	59	98	-	View	-
❌ cageseq	No	56	50	-	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	-
❌ radseq	No	45	42	-	View	-
❌ viralrecon	No	44	93	-	View	-
❌ meerpipe	No	44	84	-	View	-
❌ omicsgenetraitassociation	No	44	30	-	View	-
❌ deepmutscan	No	43	89	-	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	-
❌ abotyper	No	26	64	-	View	-
❌ riboseq	No	26	55	-	View	-
❌ scrnaseq	No	23	95	-	View	-
❌ sammyseq	No	21	148	-	View	-
❌ hic	No	21	61	-	View	-
❌ mcmicro	No	21	48	-	View	-
❌ metapep	No	20	51	-	View	-
❌ datasync	No	19	20	-	View	-
❌ mhcquant	No	18	47	-	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	-
❌ differentialabundance	No	12	47	-	View	-
❌ coproid	No	12	46	-	View	-
❌ spatialxe	No	11	116	-	View	-
❌ smrnaseq	No	11	74	-	View	-
❌ hgtseq	No	10	69	-	View	-
❌ deepmodeloptim	No	10	49	-	View	-
❌ variantbenchmarking	No	10	29	-	View	-
❌ tumourevo	No	9	60	-	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	-
❌ sopa	No	7	13	-	View	-
❌ tfactivity	No	6	57	-	View	-
❌ cellpainting	No	6	35	-	View	-
❌ pacvar	No	6	29	-	View	-
❌ fetchngs	No	6	25	-	View	-
❌ kmermaid	No	6	16	-	View	-
❌ mitodetect	No	6	16	-	View	-
❌ panoramaseq	No	6	16	-	View	-
❌ troughgraph	No	6	16	-	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	-
❌ lsmquant	No	1	41	-	View	-
❌ seqsubmit	No	1	16	-	View	-
❌ longraredisease	No	0	182	No	View	View
❌ atacseq	No	0	177	No	View	View
✅ taxprofiler	No	0	99	Yes	View	View
✅ funcscan	No	0	87	Yes	View	View
❌ methylong	No	0	81	No	View	View
✅ chipseq	No	0	69	Yes	View	View
❌ molkart	No	0	42	No	View	View
❌ stableexpression	No	0	34	No	View	View
✅ createtaxdb	No	0	33	Yes	View	View
❌ isoseq	No	0	31	No	View	View
❌ references	No	0	31	No	View	View
✅ mag	No	0	28	Yes	View	View
❌ scdownstream	No	0	27	No	View	View
❌ alleleexpression	No	0	20	No	View	View
✅ bacass	No	0	17	Yes	View	View
✅ ampliseq	No	0	16	Yes	View	View
❌ createpanelrefs	No	0	16	No	View	View
❌ genephylomodeler	No	0	10	No	View	View
❌ hlatyping	No	0	9	No	View	View
❌ gwas	No	0	7	No	View	View
✅ rnaseq	No	0	7	Yes	View	View
❌ epitopeprediction	No	0	5	No	View	View
❌ fastquorum	No	0	5	No	View	View
❌ ncrnannotator	No	0	4	No	View	View
✅ genomicrelatedness	No	0	3	Yes	View	View
✅ proteinfamilies	No	0	3	Yes	View	View
❌ raredisease	No	0	3	No	View	View
❌ ribomsqc	No	0	2	No	View	View
✅ rangeland	No	0	1	Yes	View	View
✅ bamtofastq	No	0	0	Yes	View	View
✅ demo	No	0	0	Yes	View	View
❌ demultiplex	No	0	0	No	View	View
✅ drop	No	0	0	Yes	View	View
✅ magmap	No	0	0	Yes	View	View
✅ metatdenovo	No	0	0	Yes	View	View
✅ nanostring	No	0	0	Yes	View	View
❌ phaseimpute	No	0	0	No	View	View
✅ pixelator	No	0	0	Yes	View	View
✅ proteinannotator	No	0	0	Yes	View	View
✅ rnavar	No	0	0	Yes	View	View
✅ seqinspector	No	0	0	Yes	View	View
✅ spatialvi	No	0	0	Yes	View	View
✅ variantprioritization	No	0	0	Yes	View	View
✅ viralmetagenome	No	0	0	Yes	View	View

Modules

• Total: 0 parse errors, 0 errors, 1 warnings across 1759 modules
• Zero errors: 1759 modules (100.0%)

Errors	Warnings

Module Results (0 modules with errors)

Module	Parse Error	Errors	Warnings	Lint Output

Modules with zero errors are not shown above (1759 modules). They may still have warnings. See the modules results directory for all lint outputs.

Subworkflows

• Total: 0 parse errors, 0 errors, 1 warnings across 113 subworkflows
• Zero errors: 113 subworkflows (100.0%)

Errors	Warnings

Subworkflow Results (0 subworkflows with errors)

Subworkflow	Parse Error	Errors	Warnings	Lint Output

Subworkflows with zero errors are not shown above (113 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.