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‎README.md‎

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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:** 2026-03-02 00:06:30 UTC
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- **Last updated:** 2026-03-03 00:11:18 UTC
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- **Nextflow version:** 26.02.0-edge
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## Pipelines
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- **Total:** 0 parse errors, 80 errors, 191 warnings across 19 pipelines
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- **Zero errors:** 15 pipelines (78.9%)
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- **Total:** 0 parse errors, 67 errors, 144 warnings across 19 pipelines
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- **Zero errors:** 16 pipelines (84.2%)
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| Errors | Warnings |
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| :------------------------------------------: | :----------------------------------------------: |
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| Pipeline | Parse Error | Errors | Warnings | Prints Help | Lint Output | Help Output |
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| ----------------------------------------------------------------------------------------------- | :---------: | -----: | -------: | :---------: | :-----------------------------------------------------------------: | :---------------------------------------------------------------------: |
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| :x: [genealignment](https://github.com/sanger-tol/genealignment) | No | 61 | 28 | - | [View](lint_results/pipeline-results/genealignment_lint.md) | - |
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| :x: [curationpretext](https://github.com/sanger-tol/curationpretext) | No | 13 | 53 | - | [View](lint_results/pipeline-results/curationpretext_lint.md) | - |
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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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| :white_check_mark: [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: [curationpretext](https://github.com/sanger-tol/curationpretext) | No | 0 | 6 | No | [View](lint_results/pipeline-results/curationpretext_lint.md) | [View](lint_results/prints-help-results/curationpretext_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: [genomeassembly](https://github.com/sanger-tol/genomeassembly) | No | 0 | 1 | Yes | [View](lint_results/pipeline-results/genomeassembly_lint.md) | [View](lint_results/prints-help-results/genomeassembly_help.txt) |
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## Subworkflows
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- **Total:** 0 parse errors, 0 errors, 2 warnings across 16 subworkflows
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- **Total:** 0 parse errors, 0 errors, 4 warnings across 16 subworkflows
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- **Zero errors:** 16 subworkflows (100.0%)
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| Errors | Warnings |
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| Subworkflow | Parse Error | Errors | Warnings | Lint Output |
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| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :---------: | -----: | -------: | :---------------------------------------------------------------------------------------: |
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| :white_check_mark: [gap_finder](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/gap_finder) | No | 0 | 2 | [View](lint_results/subworkflow-results/gap_finder_lint.md) |
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| :white_check_mark: [telo_finder](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/telo_finder) | No | 0 | 2 | [View](lint_results/subworkflow-results/telo_finder_lint.md) |
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| :white_check_mark: [ancestral_annotation](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/ancestral_annotation) | No | 0 | 0 | [View](lint_results/subworkflow-results/ancestral_annotation_lint.md) |
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| :white_check_mark: [bam2cool](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/bam2cool) | No | 0 | 0 | [View](lint_results/subworkflow-results/bam2cool_lint.md) |
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| :white_check_mark: [bam_samtools_merge_markdup](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/bam_samtools_merge_markdup) | No | 0 | 0 | [View](lint_results/subworkflow-results/bam_samtools_merge_markdup_lint.md) |
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| :white_check_mark: [pacbio_preprocess](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/pacbio_preprocess) | No | 0 | 0 | [View](lint_results/subworkflow-results/pacbio_preprocess_lint.md) |
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| :white_check_mark: [pairs_create_contact_maps](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/pairs_create_contact_maps) | No | 0 | 0 | [View](lint_results/subworkflow-results/pairs_create_contact_maps_lint.md) |
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| :white_check_mark: [soft_masked_fasta_repeats](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/soft_masked_fasta_repeats) | No | 0 | 0 | [View](lint_results/subworkflow-results/soft_masked_fasta_repeats_lint.md) |
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| :white_check_mark: [telo_finder](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/telo_finder) | No | 0 | 0 | [View](lint_results/subworkflow-results/telo_finder_lint.md) |
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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: 2026-03-02T00:06:10.080220+00:00
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- Generated: 2026-03-03T00:11:02.909889+00:00
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- Nextflow version: 26.02.0-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: 2026-03-02T00:06:10.080383+00:00
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- Generated: 2026-03-03T00:11:02.910066+00:00
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- Nextflow version: 26.02.0-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: 2026-03-02T00:06:10.080504+00:00
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- Generated: 2026-03-03T00:11:02.910197+00:00
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- Nextflow version: 26.02.0-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: 2026-03-02T00:06:10.080645+00:00
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- Generated: 2026-03-03T00:11:02.910352+00:00
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- Nextflow version: 26.02.0-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: 2026-03-02T00:06:10.080771+00:00
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- Generated: 2026-03-03T00:11:02.910468+00:00
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- Nextflow version: 26.02.0-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: 2026-03-02T00:06:10.080898+00:00
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- Generated: 2026-03-03T00:11:02.910603+00:00
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- Nextflow version: 26.02.0-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: 2026-03-02T00:06:10.080999+00:00
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- Generated: 2026-03-03T00:11:02.910727+00:00
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- Nextflow version: 26.02.0-edge
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- Summary: No issues found

‎lint_results/module-results/cramalign_bwamem2alignhic_lint.md‎

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# Nextflow lint results
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- Generated: 2026-03-02T00:06:10.081138+00:00
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- Generated: 2026-03-03T00:11:02.910851+00:00
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- Nextflow version: 26.02.0-edge
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- Summary: No issues found

‎lint_results/module-results/cramalign_gencramchunks_lint.md‎

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# Nextflow lint results
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- Generated: 2026-03-02T00:06:10.081334+00:00
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- Generated: 2026-03-03T00:11:02.910971+00:00
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- Nextflow version: 26.02.0-edge
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- Summary: No issues found

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