sanger-tol Strict Syntax Health Report

This repository tracks the health of sanger-tol pipelines, modules, and subworkflows with respect to Nextflow's strict syntax linting. It is a mere sanger-tol-ification of the upstream nf-core https://github.com/nf-core/strict-syntax-health.

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 sanger-tol 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: 2026-03-27 00:12:56 UTC
• Nextflow version: 26.03.1-edge

Pipelines

• Strict syntax: 0 parse errors, 6 errors, 117 warnings across 19 pipelines
• Versions Mix: 6/19 (31.6%) pipelines do not use the ch_versions += +ch_versions.mix anti-pattern
• Zero issues: 11 pipelines (57.9%)

Errors	Warnings

Pipeline Versions Mix

Pipeline Results (19 pipelines)

Pipeline	Parse Error	Errors	Warnings	Prints Help	Versions Mix	Lint Output	Help Output
❌ zippypretext	No	5	15	-	❎	View	-
❌ ascc	No	1	7	-	❎	View	-
❌ ear	No	0	52	No	❎	View	View
❌ nfmicrofinder	No	0	21	No	❎	View	View
❌ tollongc	No	0	8	No	✅	View	View
❌ blobtoolkit	No	0	7	Yes	❎	View	View
❌ purging	No	0	5	No	✅	View	View
❌ treeval	No	0	2	No	❎	View	View
✅ curationpretext	No	0	0	Yes	✅	View	View
✅ ensemblgenedownload	No	0	0	Yes	✅	View	View
✅ ensemblrepeatdownload	No	0	0	Yes	✅	View	View
✅ genomeassembly	No	0	0	Yes	❎	View	View
✅ genomenote	No	0	0	Yes	❎	View	View
✅ insdcdownload	No	0	0	Yes	✅	View	View
✅ metagenomeassembly	No	0	0	Yes	❎	View	View
✅ readmapping	No	0	0	Yes	❎	View	View
✅ sequencecomposition	No	0	0	Yes	❎	View	View
✅ variantcalling	No	0	0	Yes	❎	View	View
✅ variantcomposition	No	0	0	Yes	❎	View	View

Modules

• Strict syntax: 0 parse errors, 0 errors, 0 warnings across 32 modules
• Topic + Version: 32/32 (100.0%) modules have topics: and versions: in meta.yml
• Zero errors: 32 modules (100.0%)

Errors	Warnings

Module Topic Version Usage

Module Results (32 modules)

Module	Parse Error	Errors	Warnings	topics:	versions:	Lint Output
✅ ancestral_extract	No	0	0	✅	✅	View
✅ ancestral_plot	No	0	0	✅	✅	View
✅ asmstats	No	0	0	✅	✅	View
✅ bedchunks_create	No	0	0	✅	✅	View
✅ bedtools_bamtobedsort	No	0	0	✅	✅	View
✅ bgziptabix	No	0	0	✅	✅	View
✅ blast_blastn	No	0	0	✅	✅	View
✅ blobtoolkit_generatecsv	No	0	0	✅	✅	View
✅ blobtoolkit_generateparamsfile	No	0	0	✅	✅	View
✅ contactbed	No	0	0	✅	✅	View
✅ cramalign_bwamem2alignhic	No	0	0	✅	✅	View
✅ cramalign_gencramchunks	No	0	0	✅	✅	View
✅ cramalign_minimap2align	No	0	0	✅	✅	View
✅ cramalign_minimap2alignhic	No	0	0	✅	✅	View
✅ curationpretext_generateparamsfile	No	0	0	✅	✅	View
✅ fastxalign_minimap2align	No	0	0	✅	✅	View
✅ fastxalign_pyfastxindex	No	0	0	✅	✅	View
✅ generatecontactsindex	No	0	0	✅	✅	View
✅ gnk_fastasort	No	0	0	✅	✅	View
✅ hifiasm	No	0	0	✅	✅	View
✅ longranger_align	No	0	0	✅	✅	View
✅ longranger_mkref	No	0	0	✅	✅	View
✅ mask_softmask2bed	No	0	0	✅	✅	View
✅ mask_unmask	No	0	0	✅	✅	View
✅ pretextannotate	No	0	0	✅	✅	View
✅ restructurebuscodir	No	0	0	✅	✅	View
✅ samtools_mergedup	No	0	0	✅	✅	View
✅ telomere_extract	No	0	0	✅	✅	View
✅ telomere_regions	No	0	0	✅	✅	View
✅ telomere_windows	No	0	0	✅	✅	View
✅ yahs_makepairsfile	No	0	0	✅	✅	View
✅ yak_count	No	0	0	✅	✅	View

Subworkflows

• Strict syntax: 0 parse errors, 0 errors, 0 warnings across 20 subworkflows
• Versions channel: 20/20 (100.0%) subworkflows do not emit a versions output channel
• Zero errors: 20 subworkflows (100.0%)

Errors	Warnings

Subworkflow Results (20 subworkflows)

Subworkflow	Parse Error	Errors	Warnings	versions channel	Lint Output
✅ ancestral_annotation	No	0	0	✅	View
✅ bam2cool	No	0	0	✅	View
✅ bam_samtools_merge_markdup	No	0	0	✅	View
✅ cram_map_illumina_hic	No	0	0	✅	View
✅ cram_map_long_reads	No	0	0	✅	View
✅ fasta_10x_polishing_longranger_freebayes	No	0	0	✅	View
✅ fasta_bam_scaffolding_yahs	No	0	0	✅	View
✅ fasta_compress_index	No	0	0	✅	View
✅ fasta_purge_retained_haplotype	No	0	0	✅	View
✅ fastx_map_long_reads	No	0	0	✅	View
✅ feature_density	No	0	0	✅	View
✅ gap_finder	No	0	0	✅	View
✅ genome_statistics	No	0	0	✅	View
✅ get_blobtk_plots	No	0	0	✅	View
✅ pacbio_preprocess	No	0	0	✅	View
✅ pairs_create_contact_maps	No	0	0	✅	View
✅ repeat_density	No	0	0	✅	View
✅ repeat_masking	No	0	0	✅	View
✅ soft_masked_fasta_repeats	No	0	0	✅	View
✅ telo_finder	No	0	0	✅	View

About

This report is generated daily by running nextflow lint on each sanger-tol 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.