Update lint results [skip ci]

github-actions[bot] · github-actions[bot] · commit fc813fe8dfd7 · 2026-03-24T08:26:32.000Z
diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@ The goal is for all sanger-tol pipelines to run without errors using strict synt
 > See the [nf-core blog post](https://nf-co.re/blog/2025/nextflow_syntax_nf-core_roadmap) for details on the migration timeline.
 > **Fixing all errors from `nextflow lint` will be a requirement by early spring 2026.**
 
-- **Last updated:** 2026-03-24 00:14:55 UTC
+- **Last updated:** 2026-03-24 08:26:26 UTC
 - **Nextflow version:** 26.03.0-edge
 
 ## Pipelines
@@ -34,25 +34,25 @@ The goal is for all sanger-tol pipelines to run without errors using strict synt
 
 | Pipeline                                                                                        | Parse Error | Errors | Warnings | Prints Help |    Versions Mix    |                             Lint Output                             |                               Help Output                               |
 | ----------------------------------------------------------------------------------------------- | :---------: | -----: | -------: | :---------: | :----------------: | :-----------------------------------------------------------------: | :---------------------------------------------------------------------: |
-| :x: [zippypretext](https://github.com/sanger-tol/zippypretext)                                  |     No      |      5 |       15 |      -      |        :x:         |     [View](lint_results/pipeline-results/zippypretext_lint.md)      |                                    -                                    |
-| :x: [ascc](https://github.com/sanger-tol/ascc)                                                  |     No      |      1 |        7 |      -      |        :x:         |         [View](lint_results/pipeline-results/ascc_lint.md)          |                                    -                                    |
-| :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)          |
-| :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)     |
-| :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)        |
-| :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)      |
-| :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)        |
-| :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)        |
-| :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)    |
-| :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)  |
-| :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) |
-| :x: [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)     |
-| :x: [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)       |
-| :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)     |
-| :x: [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)   |
-| :x: [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)      |
-| :x: [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)  |
-| :x: [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)     |
-| :x: [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)   |
+| :x: [zippypretext](https://github.com/sanger-tol/zippypretext)                                  |     No      |      5 |       15 |      -      | :white_check_mark: |     [View](lint_results/pipeline-results/zippypretext_lint.md)      |                                    -                                    |
+| :x: [ascc](https://github.com/sanger-tol/ascc)                                                  |     No      |      1 |        7 |      -      | :white_check_mark: |         [View](lint_results/pipeline-results/ascc_lint.md)          |                                    -                                    |
+| :x: [ear](https://github.com/sanger-tol/ear)                                                    |     No      |      0 |       52 |     No      | :white_check_mark: |          [View](lint_results/pipeline-results/ear_lint.md)          |          [View](lint_results/prints-help-results/ear_help.txt)          |
+| :x: [nfmicrofinder](https://github.com/sanger-tol/nfmicrofinder)                                |     No      |      0 |       21 |     No      | :white_check_mark: |     [View](lint_results/pipeline-results/nfmicrofinder_lint.md)     |     [View](lint_results/prints-help-results/nfmicrofinder_help.txt)     |
+| :x: [tollongc](https://github.com/sanger-tol/tollongc)                                          |     No      |      0 |        8 |     No      |        :x:         |       [View](lint_results/pipeline-results/tollongc_lint.md)        |       [View](lint_results/prints-help-results/tollongc_help.txt)        |
+| :x: [blobtoolkit](https://github.com/sanger-tol/blobtoolkit)                                    |     No      |      0 |        7 |     Yes     | :white_check_mark: |      [View](lint_results/pipeline-results/blobtoolkit_lint.md)      |      [View](lint_results/prints-help-results/blobtoolkit_help.txt)      |
+| :x: [purging](https://github.com/sanger-tol/purging)                                            |     No      |      0 |        5 |     No      |        :x:         |        [View](lint_results/pipeline-results/purging_lint.md)        |        [View](lint_results/prints-help-results/purging_help.txt)        |
+| :x: [treeval](https://github.com/sanger-tol/treeval)                                            |     No      |      0 |        2 |     No      | :white_check_mark: |        [View](lint_results/pipeline-results/treeval_lint.md)        |        [View](lint_results/prints-help-results/treeval_help.txt)        |
+| :white_check_mark: [curationpretext](https://github.com/sanger-tol/curationpretext)             |     No      |      0 |        0 |     Yes     |        :x:         |    [View](lint_results/pipeline-results/curationpretext_lint.md)    |    [View](lint_results/prints-help-results/curationpretext_help.txt)    |
+| :white_check_mark: [ensemblgenedownload](https://github.com/sanger-tol/ensemblgenedownload)     |     No      |      0 |        0 |     Yes     |        :x:         |  [View](lint_results/pipeline-results/ensemblgenedownload_lint.md)  |  [View](lint_results/prints-help-results/ensemblgenedownload_help.txt)  |
+| :white_check_mark: [ensemblrepeatdownload](https://github.com/sanger-tol/ensemblrepeatdownload) |     No      |      0 |        0 |     Yes     |        :x:         | [View](lint_results/pipeline-results/ensemblrepeatdownload_lint.md) | [View](lint_results/prints-help-results/ensemblrepeatdownload_help.txt) |
+| :x: [genomeassembly](https://github.com/sanger-tol/genomeassembly)                              |     No      |      0 |        0 |     Yes     | :white_check_mark: |    [View](lint_results/pipeline-results/genomeassembly_lint.md)     |    [View](lint_results/prints-help-results/genomeassembly_help.txt)     |
+| :x: [genomenote](https://github.com/sanger-tol/genomenote)                                      |     No      |      0 |        0 |     Yes     | :white_check_mark: |      [View](lint_results/pipeline-results/genomenote_lint.md)       |      [View](lint_results/prints-help-results/genomenote_help.txt)       |
+| :white_check_mark: [insdcdownload](https://github.com/sanger-tol/insdcdownload)                 |     No      |      0 |        0 |     Yes     |        :x:         |     [View](lint_results/pipeline-results/insdcdownload_lint.md)     |     [View](lint_results/prints-help-results/insdcdownload_help.txt)     |
+| :x: [metagenomeassembly](https://github.com/sanger-tol/metagenomeassembly)                      |     No      |      0 |        0 |     Yes     | :white_check_mark: |  [View](lint_results/pipeline-results/metagenomeassembly_lint.md)   |  [View](lint_results/prints-help-results/metagenomeassembly_help.txt)   |
+| :x: [readmapping](https://github.com/sanger-tol/readmapping)                                    |     No      |      0 |        0 |     Yes     | :white_check_mark: |      [View](lint_results/pipeline-results/readmapping_lint.md)      |      [View](lint_results/prints-help-results/readmapping_help.txt)      |
+| :x: [sequencecomposition](https://github.com/sanger-tol/sequencecomposition)                    |     No      |      0 |        0 |     Yes     | :white_check_mark: |  [View](lint_results/pipeline-results/sequencecomposition_lint.md)  |  [View](lint_results/prints-help-results/sequencecomposition_help.txt)  |
+| :x: [variantcalling](https://github.com/sanger-tol/variantcalling)                              |     No      |      0 |        0 |     Yes     | :white_check_mark: |    [View](lint_results/pipeline-results/variantcalling_lint.md)     |    [View](lint_results/prints-help-results/variantcalling_help.txt)     |
+| :x: [variantcomposition](https://github.com/sanger-tol/variantcomposition)                      |     No      |      0 |        0 |     Yes     | :white_check_mark: |  [View](lint_results/pipeline-results/variantcomposition_lint.md)   |  [View](lint_results/prints-help-results/variantcomposition_help.txt)   |
 
 </details>
 
diff --git a/lint_results/module-results/ancestral_extract_lint.md b/lint_results/module-results/ancestral_extract_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.535901+00:00
+- Generated: 2026-03-24T08:26:04.266565+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/ancestral_plot_lint.md b/lint_results/module-results/ancestral_plot_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.536039+00:00
+- Generated: 2026-03-24T08:26:04.266748+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/asmstats_lint.md b/lint_results/module-results/asmstats_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.536117+00:00
+- Generated: 2026-03-24T08:26:04.266861+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/bedchunks_create_lint.md b/lint_results/module-results/bedchunks_create_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.536175+00:00
+- Generated: 2026-03-24T08:26:04.266988+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/bedtools_bamtobedsort_lint.md b/lint_results/module-results/bedtools_bamtobedsort_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.536241+00:00
+- Generated: 2026-03-24T08:26:04.267129+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/bgziptabix_lint.md b/lint_results/module-results/bgziptabix_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.536313+00:00
+- Generated: 2026-03-24T08:26:04.267238+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/blast_blastn_lint.md b/lint_results/module-results/blast_blastn_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.536385+00:00
+- Generated: 2026-03-24T08:26:04.267342+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/blobtoolkit_generatecsv_lint.md b/lint_results/module-results/blobtoolkit_generatecsv_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.536495+00:00
+- Generated: 2026-03-24T08:26:04.267441+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/blobtoolkit_generateparamsfile_lint.md b/lint_results/module-results/blobtoolkit_generateparamsfile_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.536585+00:00
+- Generated: 2026-03-24T08:26:04.267538+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/contactbed_lint.md b/lint_results/module-results/contactbed_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.536638+00:00
+- Generated: 2026-03-24T08:26:04.287220+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/cramalign_bwamem2alignhic_lint.md b/lint_results/module-results/cramalign_bwamem2alignhic_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.536686+00:00
+- Generated: 2026-03-24T08:26:04.287361+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/cramalign_gencramchunks_lint.md b/lint_results/module-results/cramalign_gencramchunks_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.536771+00:00
+- Generated: 2026-03-24T08:26:04.287486+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/cramalign_minimap2align_lint.md b/lint_results/module-results/cramalign_minimap2align_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.537924+00:00
+- Generated: 2026-03-24T08:26:04.287608+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/cramalign_minimap2alignhic_lint.md b/lint_results/module-results/cramalign_minimap2alignhic_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538025+00:00
+- Generated: 2026-03-24T08:26:04.287730+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/curationpretext_generateparamsfile_lint.md b/lint_results/module-results/curationpretext_generateparamsfile_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538097+00:00
+- Generated: 2026-03-24T08:26:04.287850+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/fastxalign_minimap2align_lint.md b/lint_results/module-results/fastxalign_minimap2align_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538167+00:00
+- Generated: 2026-03-24T08:26:04.287987+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/fastxalign_pyfastxindex_lint.md b/lint_results/module-results/fastxalign_pyfastxindex_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538234+00:00
+- Generated: 2026-03-24T08:26:04.288111+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/generatecontactsindex_lint.md b/lint_results/module-results/generatecontactsindex_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538307+00:00
+- Generated: 2026-03-24T08:26:04.288231+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/gnk_fastasort_lint.md b/lint_results/module-results/gnk_fastasort_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538376+00:00
+- Generated: 2026-03-24T08:26:04.288351+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/hifiasm_lint.md b/lint_results/module-results/hifiasm_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538464+00:00
+- Generated: 2026-03-24T08:26:04.288470+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/longranger_align_lint.md b/lint_results/module-results/longranger_align_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538541+00:00
+- Generated: 2026-03-24T08:26:04.288590+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/longranger_mkref_lint.md b/lint_results/module-results/longranger_mkref_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538616+00:00
+- Generated: 2026-03-24T08:26:04.288708+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/mask_softmask2bed_lint.md b/lint_results/module-results/mask_softmask2bed_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538686+00:00
+- Generated: 2026-03-24T08:26:04.288828+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/mask_unmask_lint.md b/lint_results/module-results/mask_unmask_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538759+00:00
+- Generated: 2026-03-24T08:26:04.288945+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/pretextannotate_lint.md b/lint_results/module-results/pretextannotate_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538829+00:00
+- Generated: 2026-03-24T08:26:04.289069+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/restructurebuscodir_lint.md b/lint_results/module-results/restructurebuscodir_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538899+00:00
+- Generated: 2026-03-24T08:26:04.289207+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/samtools_mergedup_lint.md b/lint_results/module-results/samtools_mergedup_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.538971+00:00
+- Generated: 2026-03-24T08:26:04.289327+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/telomere_extract_lint.md b/lint_results/module-results/telomere_extract_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.539043+00:00
+- Generated: 2026-03-24T08:26:04.289448+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/telomere_regions_lint.md b/lint_results/module-results/telomere_regions_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.539106+00:00
+- Generated: 2026-03-24T08:26:04.289567+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/telomere_windows_lint.md b/lint_results/module-results/telomere_windows_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.539172+00:00
+- Generated: 2026-03-24T08:26:04.289686+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/yahs_makepairsfile_lint.md b/lint_results/module-results/yahs_makepairsfile_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.539238+00:00
+- Generated: 2026-03-24T08:26:04.289806+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/yak_count_lint.md b/lint_results/module-results/yak_count_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:23.539306+00:00
+- Generated: 2026-03-24T08:26:04.289927+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/ancestral_annotation_lint.md b/lint_results/subworkflow-results/ancestral_annotation_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:27.446475+00:00
+- Generated: 2026-03-24T08:26:08.415616+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/bam2cool_lint.md b/lint_results/subworkflow-results/bam2cool_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:27.446639+00:00
+- Generated: 2026-03-24T08:26:08.415775+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/bam_samtools_merge_markdup_lint.md b/lint_results/subworkflow-results/bam_samtools_merge_markdup_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:27.446726+00:00
+- Generated: 2026-03-24T08:26:08.415888+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/cram_map_illumina_hic_lint.md b/lint_results/subworkflow-results/cram_map_illumina_hic_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-24T00:14:27.446781+00:00
+- Generated: 2026-03-24T08:26:08.416025+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/cram_map_long_reads_lint.md b/lint_results/subworkflow-results/cram_map_long_reads_lint.md
diff --git a/lint_results/subworkflow-results/fasta_10x_polishing_longranger_freebayes_lint.md b/lint_results/subworkflow-results/fasta_10x_polishing_longranger_freebayes_lint.md
diff --git a/lint_results/subworkflow-results/fasta_bam_scaffolding_yahs_lint.md b/lint_results/subworkflow-results/fasta_bam_scaffolding_yahs_lint.md
diff --git a/lint_results/subworkflow-results/fasta_compress_index_lint.md b/lint_results/subworkflow-results/fasta_compress_index_lint.md
diff --git a/lint_results/subworkflow-results/fasta_purge_retained_haplotype_lint.md b/lint_results/subworkflow-results/fasta_purge_retained_haplotype_lint.md
diff --git a/lint_results/subworkflow-results/fastx_map_long_reads_lint.md b/lint_results/subworkflow-results/fastx_map_long_reads_lint.md
diff --git a/lint_results/subworkflow-results/feature_density_lint.md b/lint_results/subworkflow-results/feature_density_lint.md
diff --git a/lint_results/subworkflow-results/gap_finder_lint.md b/lint_results/subworkflow-results/gap_finder_lint.md
diff --git a/lint_results/subworkflow-results/genome_statistics_lint.md b/lint_results/subworkflow-results/genome_statistics_lint.md
diff --git a/lint_results/subworkflow-results/get_blobtk_plots_lint.md b/lint_results/subworkflow-results/get_blobtk_plots_lint.md
diff --git a/lint_results/subworkflow-results/pacbio_preprocess_lint.md b/lint_results/subworkflow-results/pacbio_preprocess_lint.md
diff --git a/lint_results/subworkflow-results/pairs_create_contact_maps_lint.md b/lint_results/subworkflow-results/pairs_create_contact_maps_lint.md
diff --git a/lint_results/subworkflow-results/repeat_density_lint.md b/lint_results/subworkflow-results/repeat_density_lint.md
diff --git a/lint_results/subworkflow-results/repeat_masking_lint.md b/lint_results/subworkflow-results/repeat_masking_lint.md
diff --git a/lint_results/subworkflow-results/soft_masked_fasta_repeats_lint.md b/lint_results/subworkflow-results/soft_masked_fasta_repeats_lint.md
diff --git a/lint_results/subworkflow-results/telo_finder_lint.md b/lint_results/subworkflow-results/telo_finder_lint.md
