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: 2026-06-27 00:46:03 UTC
• Nextflow version: 26.05.0-edge

Pipelines

• Total: 0 parse errors, 1514 errors, 7488 warnings across 139 pipelines
• Zero errors: 84 pipelines (60.4%)

Errors	Warnings

Pipeline Results (139 pipelines)

Pipeline	Parse Error	Errors	Warnings	Prints Help	Lint Output	Help Output
❌ eager	No	117	367	-	View	-
❌ genomeannotator	No	79	151	-	View	-
❌ hicar	No	78	123	-	View	-
❌ evexplorer	No	74	55	-	View	-
❌ oncoanalyser	No	64	112	-	View	-
❌ viralintegration	No	64	15	-	View	-
❌ phageannotator	No	58	104	-	View	-
❌ readsimulator	No	53	53	-	View	-
❌ metaboigniter	No	52	125	-	View	-
❌ spinningjenny	No	50	12	-	View	-
❌ variantcatalogue	No	46	49	-	View	-
❌ imcyto	No	45	14	-	View	-
❌ meerpipe	No	44	85	-	View	-
❌ callingcards	No	41	177	-	View	-
❌ radseq	No	41	44	-	View	-
❌ lncpipe	No	40	180	-	View	-
❌ nascent	No	38	167	-	View	-
❌ marsseq	No	37	69	-	View	-
❌ nanoseq	No	36	80	-	View	-
❌ omicsgenetraitassociation	No	33	31	-	View	-
❌ genomeskim	No	33	14	-	View	-
❌ denovotranscript	No	31	56	-	View	-
❌ sammyseq	No	21	153	-	View	-
❌ circdna	No	21	30	-	View	-
❌ metapep	No	20	56	-	View	-
❌ bactmap	No	17	36	-	View	-
❌ slamseq	No	17	0	-	View	-
❌ pathogensurveillance	No	16	442	-	View	-
❌ deepmodeloptim	No	16	56	-	View	-
❌ diaproteomics	No	16	0	-	View	-
❌ clipseq	No	15	0	-	View	-
❌ mnaseseq	No	15	0	-	View	-
❌ proteogenomicsdb	No	15	0	-	View	-
❌ pangenome	No	14	67	-	View	-
❌ rarevariantburden	No	14	26	-	View	-
❌ detaxizer	No	13	65	-	View	-
❌ crisprseq	No	13	50	-	View	-
❌ coproid	No	12	52	-	View	-
❌ hic	No	12	31	-	View	-
❌ panoramaseq	No	11	28	-	View	-
❌ hgtseq	No	10	74	-	View	-
❌ mcmicro	No	9	80	-	View	-
❌ fastqrepair	No	9	37	-	View	-
❌ pacsomatic	No	7	120	-	View	-
❌ sopa	No	7	24	-	View	-
❌ pacvar	No	6	34	-	View	-
❌ kmermaid	No	6	21	-	View	-
❌ mitodetect	No	6	21	-	View	-
❌ troughgraph	No	6	21	-	View	-
❌ methylarray	No	4	24	-	View	-
❌ rnadnavar	No	3	382	-	View	-
❌ methylseq	No	3	69	-	View	-
❌ dualrnaseq	No	2	57	-	View	-
❌ tbanalyzer	No	2	27	-	View	-
❌ cellpainting	No	2	14	-	View	-
✅ sarek	No	0	585	Yes	View	View
✅ multiplesequencealign	No	0	178	Yes	View	View
❌ longraredisease	No	0	167	No	View	View
❌ cutandrun	No	0	160	No	View	View
✅ riboseq	No	0	160	Yes	View	View
✅ viralrecon	No	0	160	Yes	View	View
✅ diseasemodulediscovery	No	0	133	Yes	View	View
✅ differentialabundance	No	0	107	Yes	View	View
✅ taxprofiler	No	0	97	Yes	View	View
❌ deepmutscan	No	0	80	No	View	View
❌ methylong	No	0	79	No	View	View
✅ chipseq	No	0	76	Yes	View	View
✅ funcscan	No	0	70	Yes	View	View
❌ epigenomesegmentation	No	0	67	No	View	View
✅ abotyper	No	0	65	Yes	View	View
❌ tumourevo	No	0	56	No	View	View
✅ bacmodel	No	0	54	Yes	View	View
✅ mhcquant	No	0	51	Yes	View	View
❌ molkart	No	0	47	No	View	View
❌ stableexpression	No	0	43	No	View	View
✅ airrflow	No	0	40	Yes	View	View
✅ variantbenchmarking	No	0	36	Yes	View	View
✅ drugresponseeval	No	0	32	Yes	View	View
✅ scdownstream	No	0	32	Yes	View	View
✅ hadge	No	0	30	Yes	View	View
❌ rnasplice	No	0	30	No	View	View
✅ circrna	No	0	29	Yes	View	View
❌ isoseq	No	0	28	No	View	View
✅ ampliseq	No	0	27	Yes	View	View
✅ funcprofiler	No	0	25	Yes	View	View
✅ mag	No	0	25	Yes	View	View
❌ dartseq	No	0	23	No	View	View
✅ genomeassembler	No	0	23	Yes	View	View
✅ lsmquant	No	0	23	Yes	View	View
✅ bacass	No	0	21	Yes	View	View
✅ pixelator	No	0	21	Yes	View	View
❌ alleleexpression	No	0	20	No	View	View
✅ atacseq	No	0	19	Yes	View	View
❌ phaseimpute	No	0	19	No	View	View
✅ reportho	No	0	18	Yes	View	View
✅ seqsubmit	No	0	18	Yes	View	View
❌ genephylomodeler	No	0	17	No	View	View
✅ genomicrelatedness	No	0	17	Yes	View	View
✅ pairgenomealign	No	0	16	Yes	View	View
✅ fetchngs	No	0	15	Yes	View	View
✅ genomeqc	No	0	14	Yes	View	View
✅ tfactivity	No	0	14	Yes	View	View
✅ raredisease	No	0	13	Yes	View	View
✅ createtaxdb	No	0	12	Yes	View	View
❌ gwas	No	0	12	No	View	View
✅ mspepid	No	0	12	Yes	View	View
✅ fastquorum	No	0	11	Yes	View	View
✅ variantprioritization	No	0	11	Yes	View	View
✅ viralmetagenome	No	0	11	Yes	View	View
❌ ncrnannotator	No	0	10	No	View	View
✅ hlatyping	No	0	8	Yes	View	View
❌ spatialaxe	No	0	8	No	View	View
✅ spatialvi	No	0	8	Yes	View	View
✅ proteinfamilies	No	0	7	Yes	View	View
✅ proteinfold	No	0	7	Yes	View	View
✅ bamtofastq	No	0	6	Yes	View	View
✅ cageseq	No	0	6	Yes	View	View
✅ provenancereport	No	0	6	Yes	View	View
❌ ribomsqc	No	0	6	No	View	View
❌ rnafusion	No	0	6	No	View	View
✅ scrnaseq	No	0	6	Yes	View	View
✅ datasync	No	0	5	Yes	View	View
✅ drop	No	0	5	Yes	View	View
✅ magmap	No	0	5	Yes	View	View
✅ nanostring	No	0	5	Yes	View	View
✅ proteinannotator	No	0	5	Yes	View	View
✅ rangeland	No	0	5	Yes	View	View
✅ rnaseq	No	0	5	Yes	View	View
✅ scnanoseq	No	0	5	Yes	View	View
✅ demo	No	0	4	Yes	View	View
✅ demultiplex	No	0	4	Yes	View	View
✅ epitopeprediction	No	0	4	Yes	View	View
✅ metatdenovo	No	0	4	Yes	View	View
✅ phyloplace	No	0	4	Yes	View	View
❌ references	No	0	4	No	View	View
✅ rnavar	No	0	3	Yes	View	View
✅ seqinspector	No	0	3	Yes	View	View
✅ smrnaseq	No	0	3	Yes	View	View
✅ createpanelrefs	No	0	2	Yes	View	View

Workflow Outputs Migration

Adoption of the new workflow outputs syntax (a top-level output {} block) and migration away from the legacy publishDir directive. This is a separate dataset from the lint errors and warnings above.

• Uses output {}: 9 pipelines (6.5%)
• Still uses publishDir: 136 pipelines (97.8%)
• Fully migrated (output {}, no publishDir): 3 pipelines (2.2%)

Workflow Outputs Migration (139 pipelines)

The status emoji next to each pipeline shows its migration state: ✅ fully migrated (only output {}), ⚠️ in progress (output {} and publishDir), ❌ not started (only publishDir).

Pipeline	output {}	publishDir	Report
✅ createpanelrefs	Yes	No	View
✅ references	Yes	No	View
✅ seqinspector	Yes	No	View
⚠️ demultiplex	Yes	Yes (6)	View
⚠️ differentialabundance	Yes	Yes (10)	View
⚠️ proteinfamilies	Yes	Yes (73)	View
⚠️ raredisease	Yes	Yes (2)	View
⚠️ rnavar	Yes	Yes (33)	View
⚠️ sarek	Yes	Yes (186)	View
❌ abotyper	No	Yes (14)	View
❌ airrflow	No	Yes (84)	View
❌ alleleexpression	No	Yes (15)	View
❌ ampliseq	No	Yes (97)	View
❌ atacseq	No	Yes (79)	View
❌ bacass	No	Yes (33)	View
❌ bacmodel	No	Yes (14)	View
❌ bactmap	No	Yes (53)	View
❌ bamtofastq	No	Yes (17)	View
❌ cageseq	No	Yes (30)	View
❌ callingcards	No	Yes (38)	View
❌ cellpainting	No	Yes (7)	View
❌ chipseq	No	Yes (56)	View
❌ circdna	No	Yes (36)	View
❌ circrna	No	Yes (127)	View
❌ clipseq	No	Yes (24)	View
❌ coproid	No	Yes (11)	View
❌ createtaxdb	No	Yes (17)	View
❌ crisprseq	No	Yes (45)	View
❌ cutandrun	No	Yes (81)	View
❌ dartseq	No	Yes (14)	View
❌ datasync	No	Yes (2)	View
❌ deepmodeloptim	No	Yes (12)	View
❌ deepmutscan	No	Yes (21)	View
❌ demo	No	Yes (5)	View
❌ denovotranscript	No	Yes (7)	View
❌ detaxizer	No	Yes (20)	View
❌ diaproteomics	No	Yes (13)	View
❌ diseasemodulediscovery	No	Yes (21)	View
❌ drop	No	Yes (28)	View
❌ drugresponseeval	No	Yes (26)	View
❌ dualrnaseq	No	Yes (30)	View
❌ eager	No	Yes (127)	View
❌ epigenomesegmentation	No	Yes (13)	View
❌ epitopeprediction	No	Yes (18)	View
❌ evexplorer	No	Yes (9)	View
❌ fastqrepair	No	Yes (6)	View
❌ fastquorum	No	Yes (15)	View
❌ fetchngs	No	Yes (10)	View
❌ funcprofiler	No	Yes (11)	View
❌ funcscan	No	Yes (22)	View
❌ genephylomodeler	No	Yes (12)	View
❌ genomeannotator	No	Yes (14)	View
❌ genomeassembler	No	Yes (91)	View
❌ genomeqc	No	Yes (37)	View
❌ genomeskim	No	Yes (3)	View
❌ genomicrelatedness	No	Yes (61)	View
❌ gwas	No	Yes (3)	View
❌ hadge	No	Yes (33)	View
❌ hgtseq	No	Yes (50)	View
❌ hic	No	Yes (39)	View
❌ hicar	No	Yes (156)	View
❌ hlatyping	No	Yes (20)	View
❌ imcyto	No	Yes (7)	View
❌ isoseq	No	Yes (16)	View
❌ kmermaid	No	Yes (2)	View
❌ lncpipe	No	Yes (39)	View
❌ longraredisease	No	Yes (76)	View
❌ lsmquant	No	Yes (5)	View
❌ mag	No	Yes (39)	View
❌ magmap	No	Yes (27)	View
❌ marsseq	No	Yes (23)	View
❌ mcmicro	No	Yes (10)	View
❌ meerpipe	No	Yes (9)	View
❌ metaboigniter	No	Yes (31)	View
❌ metapep	No	Yes (21)	View
❌ metatdenovo	No	Yes (14)	View
❌ methylarray	No	Yes (2)	View
❌ methylong	No	Yes (41)	View
❌ methylseq	No	Yes (45)	View
❌ mhcquant	No	Yes (46)	View
❌ mitodetect	No	Yes (2)	View
❌ mnaseseq	No	Yes (26)	View
❌ molkart	No	Yes (18)	View
❌ mspepid	No	Yes (9)	View
❌ multiplesequencealign	No	Yes (17)	View
❌ nanoseq	No	Yes (3)	View
❌ nanostring	No	Yes (7)	View
❌ nascent	No	Yes (41)	View
❌ ncrnannotator	No	Yes (6)	View
❌ omicsgenetraitassociation	No	Yes (11)	View
❌ oncoanalyser	No	Yes (35)	View
❌ pacsomatic	No	Yes (40)	View
❌ pacvar	No	Yes (15)	View
❌ pairgenomealign	No	Yes (11)	View
❌ pangenome	No	Yes (30)	View
❌ panoramaseq	No	Yes (15)	View
❌ pathogensurveillance	No	Yes (52)	View
❌ phageannotator	No	Yes (39)	View
❌ phaseimpute	No	Yes (90)	View
❌ phyloplace	No	Yes (2)	View
❌ pixelator	No	Yes (12)	View
❌ proteinannotator	No	Yes (19)	View
❌ proteinfold	No	Yes (51)	View
❌ proteogenomicsdb	No	Yes (5)	View
❌ provenancereport	No	Yes (1)	View
❌ radseq	No	Yes (25)	View
❌ rangeland	No	Yes (5)	View
❌ rarevariantburden	No	Yes (17)	View
❌ readsimulator	No	Yes (18)	View
❌ reportho	No	Yes (37)	View
❌ ribomsqc	No	Yes (1)	View
❌ riboseq	No	Yes (116)	View
❌ rnadnavar	No	Yes (98)	View
❌ rnafusion	No	Yes (35)	View
❌ rnaseq	No	Yes (115)	View
❌ rnasplice	No	Yes (66)	View
❌ sammyseq	No	Yes (30)	View
❌ scdownstream	No	Yes (63)	View
❌ scnanoseq	No	Yes (92)	View
❌ scrnaseq	No	Yes (25)	View
❌ seqsubmit	No	Yes (19)	View
❌ slamseq	No	Yes (8)	View
❌ smrnaseq	No	Yes (53)	View
❌ sopa	No	Yes (4)	View
❌ spatialaxe	No	Yes (39)	View
❌ spatialvi	No	Yes (7)	View
❌ spinningjenny	No	Yes (6)	View
❌ stableexpression	No	Yes (15)	View
❌ taxprofiler	No	Yes (82)	View
❌ tbanalyzer	No	Yes (2)	View
❌ tfactivity	No	Yes (75)	View
❌ troughgraph	No	Yes (2)	View
❌ tumourevo	No	Yes (18)	View
❌ variantbenchmarking	No	Yes (79)	View
❌ variantcatalogue	No	Yes (33)	View
❌ variantprioritization	No	Yes (13)	View
❌ viralintegration	No	Yes (2)	View
❌ viralmetagenome	No	Yes (116)	View
❌ viralrecon	No	Yes (173)	View

Modules

• Total: 0 parse errors, 0 errors, 14 warnings across 1928 modules
• Zero errors: 1928 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 (1928 modules). They may still have warnings. See the modules results directory for all lint outputs.

Subworkflows

• Total: 0 parse errors, 0 errors, 26 warnings across 120 subworkflows
• Zero errors: 120 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 (120 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.
• Workflow Outputs Migration (pipelines only, shown in its own section) tracks adoption of the new workflow outputs syntax (a top-level output {} block) and migration away from the legacy publishDir directive (detected in both .nf and conf/*.config files). A pipeline is fully migrated once it uses output {} with no publishDir. Each pipeline links to a report listing exactly where both were found.

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.