Update lint results [skip ci]

github-actions[bot] · github-actions[bot] · commit f343ad6b9a2d · 2026-02-27T00:12:30.000Z
diff --git a/README.md b/README.md
@@ -12,12 +12,12 @@ 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:** 2026-02-26 00:09:52 UTC
+- **Last updated:** 2026-02-27 00:12:19 UTC
 - **Nextflow version:** 26.01.1-edge
 
 ## Pipelines
 
-- **Total:** 0 parse errors, 80 errors, 190 warnings across 19 pipelines
+- **Total:** 0 parse errors, 80 errors, 191 warnings across 19 pipelines
 - **Zero errors:** 15 pipelines (78.9%)
 
 |                    Errors                    |                     Warnings                     |
@@ -37,8 +37,8 @@ The goal is for all sanger-tol pipelines to run without errors using strict synt
 | :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)     |
 | :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)      |
 | :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)        |
+| :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)        |
 | :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)     |
-| :x: [treeval](https://github.com/sanger-tol/treeval)                                            |     No      |      0 |        1 |     No      |        [View](lint_results/pipeline-results/treeval_lint.md)        |        [View](lint_results/prints-help-results/treeval_help.txt)        |
 | :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)  |
 | :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) |
 | :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)       |
@@ -53,15 +53,15 @@ The goal is for all sanger-tol pipelines to run without errors using strict synt
 
 ## Modules
 
-- **Total:** 0 parse errors, 0 errors, 0 warnings across 22 modules
-- **Zero errors:** 22 modules (100.0%)
+- **Total:** 0 parse errors, 0 errors, 0 warnings across 24 modules
+- **Zero errors:** 24 modules (100.0%)
 
 |                   Errors                   |                    Warnings                    |
 | :----------------------------------------: | :--------------------------------------------: |
 | ![Errors](lint_results/modules_errors.png) | ![Warnings](lint_results/modules_warnings.png) |
 
 <details>
-<summary>Module Results (22 modules)</summary>
+<summary>Module Results (24 modules)</summary>
 
 | Module                                                                                                                                                                 | Parse Error | Errors | Warnings |                                  Lint Output                                   |
 | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :---------: | -----: | -------: | :----------------------------------------------------------------------------: |
@@ -81,6 +81,8 @@ The goal is for all sanger-tol pipelines to run without errors using strict synt
 | :white_check_mark: [fastxalign_pyfastxindex](https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/fastxalign/pyfastxindex)                       |     No      |      0 |        0 |      [View](lint_results/module-results/fastxalign_pyfastxindex_lint.md)       |
 | :white_check_mark: [longranger_align](https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/longranger/align)                                     |     No      |      0 |        0 |          [View](lint_results/module-results/longranger_align_lint.md)          |
 | :white_check_mark: [longranger_mkref](https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/longranger/mkref)                                     |     No      |      0 |        0 |          [View](lint_results/module-results/longranger_mkref_lint.md)          |
+| :white_check_mark: [mask_softmask2bed](https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/mask/softmask2bed)                                   |     No      |      0 |        0 |         [View](lint_results/module-results/mask_softmask2bed_lint.md)          |
+| :white_check_mark: [mask_unmask](https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/mask/unmask)                                               |     No      |      0 |        0 |            [View](lint_results/module-results/mask_unmask_lint.md)             |
 | :white_check_mark: [samtools_mergedup](https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/samtools/mergedup)                                   |     No      |      0 |        0 |         [View](lint_results/module-results/samtools_mergedup_lint.md)          |
 | :white_check_mark: [telomere_extract](https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/telomere/extract)                                     |     No      |      0 |        0 |          [View](lint_results/module-results/telomere_extract_lint.md)          |
 | :white_check_mark: [telomere_regions](https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/telomere/regions)                                     |     No      |      0 |        0 |          [View](lint_results/module-results/telomere_regions_lint.md)          |
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: 2026-02-26T00:09:38.133842+00:00
+- Generated: 2026-02-27T00:11:58.535047+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.134015+00:00
+- Generated: 2026-02-27T00:11:58.535205+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.134139+00:00
+- Generated: 2026-02-27T00:11:58.535328+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.134263+00:00
+- Generated: 2026-02-27T00:11:58.535487+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.134381+00:00
+- Generated: 2026-02-27T00:11:58.535617+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.134501+00:00
+- Generated: 2026-02-27T00:11:58.535744+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.134662+00:00
+- Generated: 2026-02-27T00:11:58.535846+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.134785+00:00
+- Generated: 2026-02-27T00:11:58.535941+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.134903+00:00
+- Generated: 2026-02-27T00:11:58.536067+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.135007+00:00
+- Generated: 2026-02-27T00:11:58.536210+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.135133+00:00
+- Generated: 2026-02-27T00:11:58.536308+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.135249+00:00
+- Generated: 2026-02-27T00:11:58.536488+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.135366+00:00
+- Generated: 2026-02-27T00:11:58.536593+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.135481+00:00
+- Generated: 2026-02-27T00:11:58.536741+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.135616+00:00
+- Generated: 2026-02-27T00:11:58.536869+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.135737+00:00
+- Generated: 2026-02-27T00:11:58.536971+00:00
 - Nextflow version: 26.01.1-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
@@ -0,0 +1,5 @@
+# Nextflow lint results
+
+- Generated: 2026-02-27T00:11:58.537115+00:00
+- Nextflow version: 26.01.1-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
@@ -0,0 +1,5 @@
+# Nextflow lint results
+
+- Generated: 2026-02-27T00:11:58.537230+00:00
+- Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.135853+00:00
+- Generated: 2026-02-27T00:11:58.537323+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.135969+00:00
+- Generated: 2026-02-27T00:11:58.537476+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.136084+00:00
+- Generated: 2026-02-27T00:11:58.537599+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.136198+00:00
+- Generated: 2026-02-27T00:11:58.537700+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.136313+00:00
+- Generated: 2026-02-27T00:11:58.537815+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:38.136428+00:00
+- Generated: 2026-02-27T00:11:58.537916+00:00
 - Nextflow version: 26.01.1-edge
 - Summary: No issues found
diff --git a/lint_results/modules_errors.png b/lint_results/modules_errors.png
diff --git a/lint_results/modules_history.json b/lint_results/modules_history.json
@@ -229,5 +229,16 @@
     "warnings_zero": 22,
     "warnings_low": 0,
     "warnings_high": 0
+  },
+  {
+    "date": "2026-02-27",
+    "total": 24,
+    "parse_errors": 0,
+    "errors_zero": 24,
+    "errors_low": 0,
+    "errors_high": 0,
+    "warnings_zero": 24,
+    "warnings_low": 0,
+    "warnings_high": 0
   }
 ]
diff --git a/lint_results/modules_results.json b/lint_results/modules_results.json
@@ -1,5 +1,5 @@
 {
-  "_repo_commit": "e7b95ba80904e8758be2c89be5e5df9e5dba3928",
+  "_repo_commit": "61c5cb9eec8b71dd5ddf151931de0784c53cf635",
   "ancestral_extract": {
     "html_url": "https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/ancestral/extract",
     "errors": 0,
@@ -96,6 +96,18 @@
     "warnings": 0,
     "parse_error": false
   },
+  "mask_softmask2bed": {
+    "html_url": "https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/mask/softmask2bed",
+    "errors": 0,
+    "warnings": 0,
+    "parse_error": false
+  },
+  "mask_unmask": {
+    "html_url": "https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/mask/unmask",
+    "errors": 0,
+    "warnings": 0,
+    "parse_error": false
+  },
   "samtools_mergedup": {
     "html_url": "https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/samtools/mergedup",
     "errors": 0,
diff --git a/lint_results/modules_warnings.png b/lint_results/modules_warnings.png
diff --git a/lint_results/pipeline-results/ascc_lint.md b/lint_results/pipeline-results/ascc_lint.md
@@ -1,7 +1,7 @@
 # Nextflow lint results
 
-- Generated: 2026-02-06T15:22:35.037428080Z
-- Nextflow version: 25.12.0-edge
+- Generated: 2026-02-27T00:11:18.670542346Z
+- Nextflow version: 26.01.1-edge
 - Summary: 1 error, 7 warnings
 
 ## :x: Errors
diff --git a/lint_results/pipeline-results/treeval_lint.md b/lint_results/pipeline-results/treeval_lint.md
@@ -1,14 +1,21 @@
 # Nextflow lint results
 
-- Generated: 2026-02-21T00:08:11.463783434Z
+- Generated: 2026-02-27T00:11:36.034985700Z
 - Nextflow version: 26.01.1-edge
-- Summary: 1 warning
+- Summary: 2 warnings
 
 ## :warning: Warnings
 
-- Warning: `subworkflows/local/generate_sorted_genome/main.nf:31:23`: Implicit closure parameter is deprecated, declare an explicit parameter instead
+- Warning: `modules/local/selfcomp/splitfasta/main.nf:25:9`: Variable was declared but not used
 
   ```nextflow
-          .view{"SIZES: $it"}
-                        ^^
+      def VERSION     = "1.7.8-1"
+          ^^^^^^^
+  ```
+
+- Warning: `modules/local/selfcomp/splitfasta/main.nf:32:9`: Variable was declared but not used
+
+  ```nextflow
+      def VERSION     = "1.7.8-1"
+          ^^^^^^^
   ```
diff --git a/lint_results/pipelines_errors.png b/lint_results/pipelines_errors.png
diff --git a/lint_results/pipelines_history.json b/lint_results/pipelines_history.json
@@ -271,5 +271,18 @@
     "warnings_high": 4,
     "prints_help_pass": 11,
     "prints_help_fail": 4
+  },
+  {
+    "date": "2026-02-27",
+    "total": 19,
+    "parse_errors": 0,
+    "errors_zero": 15,
+    "errors_low": 2,
+    "errors_high": 2,
+    "warnings_zero": 9,
+    "warnings_low": 6,
+    "warnings_high": 4,
+    "prints_help_pass": 11,
+    "prints_help_fail": 4
   }
 ]
diff --git a/lint_results/pipelines_results.json b/lint_results/pipelines_results.json
@@ -2,7 +2,7 @@
   "ascc": {
     "full_name": "sanger-tol/ascc",
     "html_url": "https://github.com/sanger-tol/ascc",
-    "commit": "4d5733ba39197ec6c991f546c6bc180827e9710e",
+    "commit": "4356e522058cf85b6c3a56a40c60f374b5f09c05",
     "errors": 1,
     "warnings": 7,
     "parse_error": false,
@@ -137,9 +137,9 @@
   "treeval": {
     "full_name": "sanger-tol/treeval",
     "html_url": "https://github.com/sanger-tol/treeval",
-    "commit": "3751dd58ee743a16700ab618311500402d0f5b85",
+    "commit": "7b40ee76404e64dae349d2e9e2a089b9c1269c08",
     "errors": 0,
-    "warnings": 1,
+    "warnings": 2,
     "parse_error": false,
     "prints_help": false
   },
diff --git a/lint_results/pipelines_warnings.png b/lint_results/pipelines_warnings.png
diff --git a/lint_results/prints-help-results/treeval_help.txt b/lint_results/prints-help-results/treeval_help.txt
@@ -4,7 +4,7 @@ $ NXF_SYNTAX_PARSER=v2 nextflow run . --help
  N E X T F L O W   ~  version 26.01.1-edge
 
 Downloading plugin nf-schema@2.5.1
-Launching `./main.nf` [nauseous_nobel] revision: 83b21d0982
+Launching `./main.nf` [ecstatic_watson] revision: 83b21d0982
 
 WARN: Unrecognized config option 'validation.defaultIgnoreParams'
 WARN: Unrecognized config option 'validation.monochromeLogs'
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: 2026-02-26T00:09:41.841282+00:00
+- Generated: 2026-02-27T00:12:02.283943+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:41.841448+00:00
+- Generated: 2026-02-27T00:12:02.284106+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:41.841575+00:00
+- Generated: 2026-02-27T00:12:02.284225+00:00
 - Nextflow version: 26.01.1-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: 2026-02-26T00:09:41.841736+00:00
+- Generated: 2026-02-27T00:12:02.284332+00:00
 - Nextflow version: 26.01.1-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
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-02-26T00:09:41.841856+00:00
+- Generated: 2026-02-27T00:12:02.284478+00:00
 - Nextflow version: 26.01.1-edge
 - Summary: No issues found
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
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-02-26T00:09:41.841975+00:00
+- Generated: 2026-02-27T00:12:02.284581+00:00
 - Nextflow version: 26.01.1-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/fasta_bam_scaffolding_yahs_lint.md b/lint_results/subworkflow-results/fasta_bam_scaffolding_yahs_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-02-26T00:09:41.842090+00:00
+- Generated: 2026-02-27T00:12:02.284699+00:00
 - Nextflow version: 26.01.1-edge
 - Summary: No issues found
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/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/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/telo_finder_lint.md b/lint_results/subworkflow-results/telo_finder_lint.md
diff --git a/lint_results/subworkflows_errors.png b/lint_results/subworkflows_errors.png
diff --git a/lint_results/subworkflows_history.json b/lint_results/subworkflows_history.json
diff --git a/lint_results/subworkflows_results.json b/lint_results/subworkflows_results.json
diff --git a/lint_results/subworkflows_warnings.png b/lint_results/subworkflows_warnings.png
