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‎README.md‎

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@@ -12,42 +12,47 @@ The goal is for all sanger-tol pipelines to run without errors using strict synt
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> See the [nf-core blog post](https://nf-co.re/blog/2025/nextflow_syntax_nf-core_roadmap) for details on the migration timeline.
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> **Fixing all errors from `nextflow lint` will be a requirement by early spring 2026.**
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- **Last updated:** 2026-03-23 00:09:29 UTC
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- **Last updated:** 2026-03-24 10:48:58 UTC
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- **Nextflow version:** 26.03.0-edge
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## Pipelines
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- **Strict syntax:** 0 parse errors, 6 errors, 117 warnings across 19 pipelines
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- **Versions Mix:** 6/19 (31.6%) pipelines do not use the `ch_versions += +ch_versions.mix` anti-pattern
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- **Zero issues:** 11 pipelines (57.9%)
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| Errors | Warnings |
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| :------------------------------------------: | :----------------------------------------------: |
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| ![Errors](lint_results/pipelines_errors.png) | ![Warnings](lint_results/pipelines_warnings.png) |
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| Pipeline Versions Mix |
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| :------------------------------------------------------: |
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| ![Versions Mix](lint_results/pipelines_versions_mix.png) |
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<details>
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<summary>Pipeline Results (19 pipelines)</summary>
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| Pipeline | Parse Error | Errors | Warnings | Prints Help | Lint Output | Help Output |
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| ----------------------------------------------------------------------------------------------- | :---------: | -----: | -------: | :---------: | :-----------------------------------------------------------------: | :---------------------------------------------------------------------: |
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| :x: [zippypretext](https://github.com/sanger-tol/zippypretext) | No | 5 | 15 | - | [View](lint_results/pipeline-results/zippypretext_lint.md) | - |
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| :x: [ascc](https://github.com/sanger-tol/ascc) | No | 1 | 7 | - | [View](lint_results/pipeline-results/ascc_lint.md) | - |
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| :x: [ear](https://github.com/sanger-tol/ear) | No | 0 | 52 | No | [View](lint_results/pipeline-results/ear_lint.md) | [View](lint_results/prints-help-results/ear_help.txt) |
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| :x: [nfmicrofinder](https://github.com/sanger-tol/nfmicrofinder) | No | 0 | 21 | No | [View](lint_results/pipeline-results/nfmicrofinder_lint.md) | [View](lint_results/prints-help-results/nfmicrofinder_help.txt) |
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| :x: [tollongc](https://github.com/sanger-tol/tollongc) | No | 0 | 8 | No | [View](lint_results/pipeline-results/tollongc_lint.md) | [View](lint_results/prints-help-results/tollongc_help.txt) |
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| :x: [blobtoolkit](https://github.com/sanger-tol/blobtoolkit) | No | 0 | 7 | Yes | [View](lint_results/pipeline-results/blobtoolkit_lint.md) | [View](lint_results/prints-help-results/blobtoolkit_help.txt) |
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| :x: [purging](https://github.com/sanger-tol/purging) | No | 0 | 5 | No | [View](lint_results/pipeline-results/purging_lint.md) | [View](lint_results/prints-help-results/purging_help.txt) |
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| :x: [treeval](https://github.com/sanger-tol/treeval) | No | 0 | 2 | No | [View](lint_results/pipeline-results/treeval_lint.md) | [View](lint_results/prints-help-results/treeval_help.txt) |
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| :white_check_mark: [curationpretext](https://github.com/sanger-tol/curationpretext) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/curationpretext_lint.md) | [View](lint_results/prints-help-results/curationpretext_help.txt) |
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| :white_check_mark: [ensemblgenedownload](https://github.com/sanger-tol/ensemblgenedownload) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/ensemblgenedownload_lint.md) | [View](lint_results/prints-help-results/ensemblgenedownload_help.txt) |
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| :white_check_mark: [ensemblrepeatdownload](https://github.com/sanger-tol/ensemblrepeatdownload) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/ensemblrepeatdownload_lint.md) | [View](lint_results/prints-help-results/ensemblrepeatdownload_help.txt) |
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| :white_check_mark: [genomeassembly](https://github.com/sanger-tol/genomeassembly) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/genomeassembly_lint.md) | [View](lint_results/prints-help-results/genomeassembly_help.txt) |
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| :white_check_mark: [genomenote](https://github.com/sanger-tol/genomenote) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/genomenote_lint.md) | [View](lint_results/prints-help-results/genomenote_help.txt) |
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| :white_check_mark: [insdcdownload](https://github.com/sanger-tol/insdcdownload) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/insdcdownload_lint.md) | [View](lint_results/prints-help-results/insdcdownload_help.txt) |
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| :white_check_mark: [metagenomeassembly](https://github.com/sanger-tol/metagenomeassembly) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/metagenomeassembly_lint.md) | [View](lint_results/prints-help-results/metagenomeassembly_help.txt) |
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| :white_check_mark: [readmapping](https://github.com/sanger-tol/readmapping) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/readmapping_lint.md) | [View](lint_results/prints-help-results/readmapping_help.txt) |
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| :white_check_mark: [sequencecomposition](https://github.com/sanger-tol/sequencecomposition) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/sequencecomposition_lint.md) | [View](lint_results/prints-help-results/sequencecomposition_help.txt) |
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| :white_check_mark: [variantcalling](https://github.com/sanger-tol/variantcalling) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/variantcalling_lint.md) | [View](lint_results/prints-help-results/variantcalling_help.txt) |
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| :white_check_mark: [variantcomposition](https://github.com/sanger-tol/variantcomposition) | No | 0 | 0 | Yes | [View](lint_results/pipeline-results/variantcomposition_lint.md) | [View](lint_results/prints-help-results/variantcomposition_help.txt) |
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| Pipeline | Parse Error | Errors | Warnings | Prints Help | Versions Mix | Lint Output | Help Output |
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| ----------------------------------------------------------------------------------------------- | :---------: | -----: | -------: | :---------: | :----------------: | :-----------------------------------------------------------------: | :---------------------------------------------------------------------: |
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| :x: [zippypretext](https://github.com/sanger-tol/zippypretext) | No | 5 | 15 | - | :x: | [View](lint_results/pipeline-results/zippypretext_lint.md) | - |
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| :x: [ascc](https://github.com/sanger-tol/ascc) | No | 1 | 7 | - | :x: | [View](lint_results/pipeline-results/ascc_lint.md) | - |
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| :x: [ear](https://github.com/sanger-tol/ear) | No | 0 | 52 | No | :x: | [View](lint_results/pipeline-results/ear_lint.md) | [View](lint_results/prints-help-results/ear_help.txt) |
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| :x: [nfmicrofinder](https://github.com/sanger-tol/nfmicrofinder) | No | 0 | 21 | No | :x: | [View](lint_results/pipeline-results/nfmicrofinder_lint.md) | [View](lint_results/prints-help-results/nfmicrofinder_help.txt) |
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| :x: [tollongc](https://github.com/sanger-tol/tollongc) | No | 0 | 8 | No | :white_check_mark: | [View](lint_results/pipeline-results/tollongc_lint.md) | [View](lint_results/prints-help-results/tollongc_help.txt) |
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| :x: [blobtoolkit](https://github.com/sanger-tol/blobtoolkit) | No | 0 | 7 | Yes | :x: | [View](lint_results/pipeline-results/blobtoolkit_lint.md) | [View](lint_results/prints-help-results/blobtoolkit_help.txt) |
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| :x: [purging](https://github.com/sanger-tol/purging) | No | 0 | 5 | No | :white_check_mark: | [View](lint_results/pipeline-results/purging_lint.md) | [View](lint_results/prints-help-results/purging_help.txt) |
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| :x: [treeval](https://github.com/sanger-tol/treeval) | No | 0 | 2 | No | :x: | [View](lint_results/pipeline-results/treeval_lint.md) | [View](lint_results/prints-help-results/treeval_help.txt) |
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| :white_check_mark: [curationpretext](https://github.com/sanger-tol/curationpretext) | No | 0 | 0 | Yes | :white_check_mark: | [View](lint_results/pipeline-results/curationpretext_lint.md) | [View](lint_results/prints-help-results/curationpretext_help.txt) |
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| :white_check_mark: [ensemblgenedownload](https://github.com/sanger-tol/ensemblgenedownload) | No | 0 | 0 | Yes | :white_check_mark: | [View](lint_results/pipeline-results/ensemblgenedownload_lint.md) | [View](lint_results/prints-help-results/ensemblgenedownload_help.txt) |
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| :white_check_mark: [ensemblrepeatdownload](https://github.com/sanger-tol/ensemblrepeatdownload) | No | 0 | 0 | Yes | :white_check_mark: | [View](lint_results/pipeline-results/ensemblrepeatdownload_lint.md) | [View](lint_results/prints-help-results/ensemblrepeatdownload_help.txt) |
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| :white_check_mark: [genomeassembly](https://github.com/sanger-tol/genomeassembly) | No | 0 | 0 | Yes | :x: | [View](lint_results/pipeline-results/genomeassembly_lint.md) | [View](lint_results/prints-help-results/genomeassembly_help.txt) |
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| :white_check_mark: [genomenote](https://github.com/sanger-tol/genomenote) | No | 0 | 0 | Yes | :x: | [View](lint_results/pipeline-results/genomenote_lint.md) | [View](lint_results/prints-help-results/genomenote_help.txt) |
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| :white_check_mark: [insdcdownload](https://github.com/sanger-tol/insdcdownload) | No | 0 | 0 | Yes | :white_check_mark: | [View](lint_results/pipeline-results/insdcdownload_lint.md) | [View](lint_results/prints-help-results/insdcdownload_help.txt) |
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| :white_check_mark: [metagenomeassembly](https://github.com/sanger-tol/metagenomeassembly) | No | 0 | 0 | Yes | :x: | [View](lint_results/pipeline-results/metagenomeassembly_lint.md) | [View](lint_results/prints-help-results/metagenomeassembly_help.txt) |
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| :white_check_mark: [readmapping](https://github.com/sanger-tol/readmapping) | No | 0 | 0 | Yes | :x: | [View](lint_results/pipeline-results/readmapping_lint.md) | [View](lint_results/prints-help-results/readmapping_help.txt) |
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| :white_check_mark: [sequencecomposition](https://github.com/sanger-tol/sequencecomposition) | No | 0 | 0 | Yes | :x: | [View](lint_results/pipeline-results/sequencecomposition_lint.md) | [View](lint_results/prints-help-results/sequencecomposition_help.txt) |
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| :white_check_mark: [variantcalling](https://github.com/sanger-tol/variantcalling) | No | 0 | 0 | Yes | :x: | [View](lint_results/pipeline-results/variantcalling_lint.md) | [View](lint_results/prints-help-results/variantcalling_help.txt) |
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| :white_check_mark: [variantcomposition](https://github.com/sanger-tol/variantcomposition) | No | 0 | 0 | Yes | :x: | [View](lint_results/pipeline-results/variantcomposition_lint.md) | [View](lint_results/prints-help-results/variantcomposition_help.txt) |
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</details>
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‎lint_results/module-results/ancestral_extract_lint.md‎

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# Nextflow lint results
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- Generated: 2026-03-23T00:09:07.376586+00:00
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- Generated: 2026-03-24T10:48:39.818892+00:00
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- Nextflow version: 26.03.0-edge
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- Summary: No issues found

‎lint_results/module-results/ancestral_plot_lint.md‎

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# Nextflow lint results
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- Generated: 2026-03-23T00:09:07.376717+00:00
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- Generated: 2026-03-24T10:48:39.819093+00:00
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- Nextflow version: 26.03.0-edge
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- Summary: No issues found

‎lint_results/module-results/asmstats_lint.md‎

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# Nextflow lint results
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- Generated: 2026-03-23T00:09:07.376783+00:00
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- Generated: 2026-03-24T10:48:39.819209+00:00
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- Nextflow version: 26.03.0-edge
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- Summary: No issues found

‎lint_results/module-results/bedchunks_create_lint.md‎

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# Nextflow lint results
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- Generated: 2026-03-23T00:09:07.387514+00:00
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- Generated: 2026-03-24T10:48:39.819310+00:00
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- Nextflow version: 26.03.0-edge
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- Summary: No issues found

‎lint_results/module-results/bedtools_bamtobedsort_lint.md‎

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# Nextflow lint results
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- Generated: 2026-03-23T00:09:07.387652+00:00
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- Generated: 2026-03-24T10:48:39.819415+00:00
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- Nextflow version: 26.03.0-edge
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- Summary: No issues found

‎lint_results/module-results/bgziptabix_lint.md‎

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# Nextflow lint results
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- Generated: 2026-03-23T00:09:07.387707+00:00
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- Generated: 2026-03-24T10:48:39.819510+00:00
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- Nextflow version: 26.03.0-edge
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- Summary: No issues found

‎lint_results/module-results/blast_blastn_lint.md‎

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# Nextflow lint results
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- Generated: 2026-03-23T00:09:07.387757+00:00
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- Generated: 2026-03-24T10:48:39.819603+00:00
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- Nextflow version: 26.03.0-edge
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- Summary: No issues found

‎lint_results/module-results/blobtoolkit_generatecsv_lint.md‎

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# Nextflow lint results
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- Generated: 2026-03-23T00:09:07.387820+00:00
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- Generated: 2026-03-24T10:48:39.819693+00:00
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- Nextflow version: 26.03.0-edge
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- Summary: No issues found

‎lint_results/module-results/blobtoolkit_generateparamsfile_lint.md‎

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# Nextflow lint results
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- Generated: 2026-03-23T00:09:07.387910+00:00
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- Generated: 2026-03-24T10:48:39.819785+00:00
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- Nextflow version: 26.03.0-edge
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- Summary: No issues found

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