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: 2026-01-22 00:21:59 UTC
• Nextflow version: 25.12.0-edge

Pipelines

• Total: 0 parse errors, 3505 errors, 10028 warnings across 130 pipelines
• Zero errors: 21 pipelines (16.2%)

Errors	Warnings

Pipeline Results (130 pipelines)

Pipeline	Parse Error	Errors	Warnings	Prints Help	Lint Output	Help Output
❌ oncoanalyser	No	305	102	-	View	-
❌ sarek	No	152	614	-	View	-
❌ airrflow	No	150	141	-	View	-
❌ deepmutscan	No	121	118	-	View	-
❌ eager	No	115	361	-	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	-
❌ demultiplex	No	54	67	-	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	-
❌ chipseq	No	47	181	-	View	-
❌ radseq	No	45	42	-	View	-
❌ meerpipe	No	44	84	-	View	-
❌ omicsgenetraitassociation	No	44	30	-	View	-
❌ viralrecon	No	43	98	-	View	-
❌ riboseq	No	42	195	-	View	-
❌ callingcards	No	41	168	-	View	-
❌ pathogensurveillance	No	40	486	-	View	-
❌ lncpipe	No	40	176	-	View	-
❌ genomeskim	No	40	13	-	View	-
❌ coproid	No	38	58	-	View	-
❌ circdna	No	38	30	-	View	-
❌ marsseq	No	37	64	-	View	-
❌ nanoseq	No	36	43	-	View	-
❌ proteomicslfq	No	36	0	-	View	-
❌ nascent	No	34	162	-	View	-
❌ genomeqc	No	34	114	-	View	-
❌ rarevariantburden	No	33	22	-	View	-
❌ rnadnavar	No	31	371	-	View	-
❌ multiplesequencealign	No	31	158	-	View	-
❌ denovotranscript	No	31	51	-	View	-
❌ raredisease	No	30	55	-	View	-
❌ bacass	No	27	131	-	View	-
❌ hic	No	27	73	-	View	-
❌ bactmap	No	27	64	-	View	-
❌ magmap	No	26	70	-	View	-
❌ abotyper	No	26	64	-	View	-
❌ scrnaseq	No	22	111	-	View	-
❌ sammyseq	No	21	148	-	View	-
❌ mcmicro	No	21	48	-	View	-
❌ rangeland	No	21	43	-	View	-
❌ epitopeprediction	No	20	22	-	View	-
❌ datasync	No	19	20	-	View	-
❌ viralmetagenome	No	18	207	-	View	-
❌ cutandrun	No	17	152	-	View	-
❌ phyloplace	No	17	106	-	View	-
❌ hlatyping	No	17	16	-	View	-
❌ slamseq	No	17	0	-	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	-
❌ differentialabundance	No	14	50	-	View	-
❌ tbanalyzer	No	14	47	-	View	-
❌ spatialvi	No	14	20	-	View	-
❌ rnafusion	No	13	116	-	View	-
❌ detaxizer	No	13	61	-	View	-
❌ crisprseq	No	13	45	-	View	-
❌ sopa	No	13	17	-	View	-
❌ variantbenchmarking	No	12	143	-	View	-
❌ drop	No	12	77	-	View	-
❌ pacvar	No	12	54	-	View	-
❌ smrnaseq	No	11	74	-	View	-
❌ metapep	No	11	34	-	View	-
❌ hgtseq	No	10	69	-	View	-
❌ pixelator	No	10	65	-	View	-
❌ deepmodeloptim	No	10	49	-	View	-
❌ mhcquant	No	9	60	-	View	-
❌ tumourevo	No	9	55	-	View	-
❌ fastqrepair	No	9	32	-	View	-
❌ pacsomatic	No	7	113	-	View	-
❌ drugresponseeval	No	7	29	-	View	-
❌ longraredisease	No	6	121	-	View	-
❌ tfactivity	No	6	57	-	View	-
❌ lsmquant	No	6	55	-	View	-
❌ cellpainting	No	6	35	-	View	-
❌ fastquorum	No	6	28	-	View	-
❌ fetchngs	No	6	25	-	View	-
❌ demo	No	6	17	-	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	-
❌ ampliseq	No	4	148	-	View	-
❌ methylseq	No	3	65	-	View	-
❌ methylarray	No	3	19	-	View	-
❌ reportho	No	2	90	-	View	-
❌ dualrnaseq	No	2	48	-	View	-
❌ pairgenomealign	No	2	24	-	View	-
❌ phaseimpute	No	1	128	-	View	-
❌ seqsubmit	No	1	32	-	View	-
❌ scdownstream	No	1	23	-	View	-
❌ seqinspector	No	1	14	-	View	-
❌ taxprofiler	No	0	113	No	View	View
❌ spatialxe	No	0	98	No	View	View
❌ methylong	No	0	81	No	View	View
❌ funcscan	No	0	73	No	View	View
❌ molkart	No	0	63	No	View	View
❌ mag	No	0	35	No	View	View
❌ createtaxdb	No	0	33	No	View	View
❌ isoseq	No	0	31	No	View	View
❌ references	No	0	31	No	View	View
❌ stableexpression	No	0	30	No	View	View
❌ ribomsqc	No	0	27	No	View	View
❌ proteinfold	No	0	25	No	View	View
❌ alleleexpression	No	0	20	No	View	View
❌ createpanelrefs	No	0	15	No	View	View
✅ rnavar	No	0	14	Yes	View	View
❌ proteinannotator	No	0	8	No	View	View
❌ bamtofastq	No	0	2	No	View	View
❌ variantprioritization	No	0	1	No	View	View
❌ nanostring	No	0	0	No	View	View
❌ proteinfamilies	No	0	0	No	View	View
❌ rnaseq	No	0	0	No	View	View

Modules

• Total: 0 parse errors, 69 errors, 630 warnings across 1361 modules
• Zero errors: 1319 modules (96.9%)

Errors	Warnings

Module Results (42 modules with errors)

Module	Parse Error	Errors	Warnings	Lint Output
❌ spaceranger_count	No	7	0	View
❌ cellranger_multi	No	4	39	View
❌ amulety_antiberta2	No	3	1	View
❌ amulety_antiberty	No	3	1	View
❌ amulety_balmpaired	No	3	1	View
❌ amulety_esm2	No	3	1	View
❌ krakentools_extractkrakenreads	No	2	5	View
❌ plink_epistasis	No	2	3	View
❌ plink_fastepistasis	No	2	3	View
❌ chewbbaca_createschema	No	2	2	View
❌ svtyper_svtyper	No	2	1	View
❌ svtyper_svtypersso	No	2	1	View
❌ biobambam_bamsormadup	No	2	0	View
❌ blobtk_plot	No	2	0	View
❌ cellrangerarc_count	No	2	0	View
❌ rastair_mbiasparser	No	2	0	View
❌ cellranger_count	No	1	2	View
❌ cellrangerarc_mkgtf	No	1	1	View
❌ cellrangerarc_mkref	No	1	1	View
❌ hmmer_hmmfetch	No	1	1	View
❌ kraken2_buildstandard	No	1	1	View
❌ ribotish_predict	No	1	1	View
❌ sam2lca_analyze	No	1	1	View
❌ shinyngs_app	No	1	1	View
❌ svanalyzer_svbenchmark	No	1	1	View
❌ cellrangeratac_mkfastq	No	1	0	View
❌ cnvnator_cnvnator	No	1	0	View
❌ dastool_scaffolds2bin	No	1	0	View
❌ dragen_germline	No	1	0	View
❌ happy_sompy	No	1	0	View
❌ ichorcna_createpon	No	1	0	View
❌ jvarkit_sam2tsv	No	1	0	View
❌ jvarkit_vcf2table	No	1	0	View
❌ kaiju_mergeoutputs	No	1	0	View
❌ metaphlan_makedb	No	1	0	View
❌ pharokka_installdatabases	No	1	0	View
❌ ribotricer_detectorfs	No	1	0	View
❌ segemehl_align	No	1	0	View
❌ star_starsolo	No	1	0	View
❌ vcfpgloader_load	No	1	0	View
❌ vg_deconstruct	No	1	0	View
❌ vsearch_sort	No	1	0	View

Modules with zero errors are not shown above (1319 modules). They may still have warnings. See the modules results directory for all lint outputs.

Subworkflows

• Total: 0 parse errors, 7 errors, 164 warnings across 102 subworkflows
• Zero errors: 98 subworkflows (96.1%)

Errors	Warnings

Subworkflow Results (4 subworkflows with errors)

Subworkflow	Parse Error	Errors	Warnings	Lint Output
❌ fastq_taxonomic_profile_metaphlan	No	4	3	View
❌ dia_proteomics_analysis	No	1	7	View
❌ bam_split_by_region	No	1	0	View
❌ fasta_index_dna	No	1	0	View

Subworkflows with zero errors are not shown above (98 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.