Update lint results [skip ci]

github-actions[bot] · github-actions[bot] · commit fdfeb9691b3f · 2026-02-28T00:08:55.000Z
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:** 2026-02-27 00:12:19 UTC
+- **Last updated:** 2026-02-28 00:08:51 UTC
 - **Nextflow version:** 26.01.1-edge
 
 ## Pipelines
@@ -94,7 +94,7 @@ The goal is for all sanger-tol pipelines to run without errors using strict synt
 
 ## Subworkflows
 
-- **Total:** 0 parse errors, 0 errors, 0 warnings across 14 subworkflows
+- **Total:** 0 parse errors, 0 errors, 2 warnings across 14 subworkflows
 - **Zero errors:** 14 subworkflows (100.0%)
 
 |                     Errors                      |                      Warnings                       |
@@ -106,6 +106,7 @@ The goal is for all sanger-tol pipelines to run without errors using strict synt
 
 | Subworkflow                                                                                                                                                                             | Parse Error | Errors | Warnings |                                        Lint Output                                        |
 | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :---------: | -----: | -------: | :---------------------------------------------------------------------------------------: |
+| :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)                |
 | :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)           |
 | :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)                 |
 | :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)        |
@@ -115,7 +116,6 @@ The goal is for all sanger-tol pipelines to run without errors using strict synt
 | :white_check_mark: [fasta_bam_scaffolding_yahs](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/fasta_bam_scaffolding_yahs)                             |     No      |      0 |        0 |        [View](lint_results/subworkflow-results/fasta_bam_scaffolding_yahs_lint.md)        |
 | :white_check_mark: [fasta_purge_retained_haplotype](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/fasta_purge_retained_haplotype)                     |     No      |      0 |        0 |      [View](lint_results/subworkflow-results/fasta_purge_retained_haplotype_lint.md)      |
 | :white_check_mark: [fastx_map_long_reads](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/fastx_map_long_reads)                                         |     No      |      0 |        0 |           [View](lint_results/subworkflow-results/fastx_map_long_reads_lint.md)           |
-| :white_check_mark: [gap_finder](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/gap_finder)                                                             |     No      |      0 |        0 |                [View](lint_results/subworkflow-results/gap_finder_lint.md)                |
 | :white_check_mark: [genome_statistics](https://github.com/sanger-tol/nf-core-modules/tree/main/subworkflows/sanger-tol/genome_statistics)                                               |     No      |      0 |        0 |            [View](lint_results/subworkflow-results/genome_statistics_lint.md)             |
 | :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)             |
 | :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)         |
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: 2026-02-27T00:11:58.535047+00:00
+- Generated: 2026-02-28T00:08:31.687689+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: 2026-02-27T00:11:58.535205+00:00
+- Generated: 2026-02-28T00:08:31.687847+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: 2026-02-27T00:11:58.535328+00:00
+- Generated: 2026-02-28T00:08:31.687954+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: 2026-02-27T00:11:58.535487+00:00
+- Generated: 2026-02-28T00:08:31.688068+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: 2026-02-27T00:11:58.535617+00:00
+- Generated: 2026-02-28T00:08:31.688181+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: 2026-02-27T00:11:58.535744+00:00
+- Generated: 2026-02-28T00:08:31.688289+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: 2026-02-27T00:11:58.535846+00:00
+- Generated: 2026-02-28T00:08:31.688382+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: 2026-02-27T00:11:58.535941+00:00
+- Generated: 2026-02-28T00:08:31.688491+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: 2026-02-27T00:11:58.536067+00:00
+- Generated: 2026-02-28T00:08:31.688660+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: 2026-02-27T00:11:58.536210+00:00
+- Generated: 2026-02-28T00:08:31.688762+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: 2026-02-27T00:11:58.536308+00:00
+- Generated: 2026-02-28T00:08:31.688879+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: 2026-02-27T00:11:58.536488+00:00
+- Generated: 2026-02-28T00:08:31.688992+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: 2026-02-27T00:11:58.536593+00:00
+- Generated: 2026-02-28T00:08:31.689093+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: 2026-02-27T00:11:58.536741+00:00
+- Generated: 2026-02-28T00:08:31.689208+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: 2026-02-27T00:11:58.536869+00:00
+- Generated: 2026-02-28T00:08:31.689303+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: 2026-02-27T00:11:58.536971+00:00
+- Generated: 2026-02-28T00:08:31.689416+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
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-02-27T00:11:58.537115+00:00
+- Generated: 2026-02-28T00:08:31.689517+00:00
 - Nextflow version: 26.01.1-edge
-- Summary: No issues found
+- 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: 2026-02-27T00:11:58.537230+00:00
+- Generated: 2026-02-28T00:08:31.689637+00:00
 - Nextflow version: 26.01.1-edge
-- Summary: No issues found
+- 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: 2026-02-27T00:11:58.537323+00:00
+- Generated: 2026-02-28T00:08:31.689757+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: 2026-02-27T00:11:58.537476+00:00
+- Generated: 2026-02-28T00:08:31.689852+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: 2026-02-27T00:11:58.537599+00:00
+- Generated: 2026-02-28T00:08:31.689951+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: 2026-02-27T00:11:58.537700+00:00
+- Generated: 2026-02-28T00:08:31.690061+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: 2026-02-27T00:11:58.537815+00:00
+- Generated: 2026-02-28T00:08:31.690156+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: 2026-02-27T00:11:58.537916+00:00
+- Generated: 2026-02-28T00:08:31.690266+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
@@ -240,5 +240,16 @@
     "warnings_zero": 24,
     "warnings_low": 0,
     "warnings_high": 0
+  },
+  {
+    "date": "2026-02-28",
+    "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": "61c5cb9eec8b71dd5ddf151931de0784c53cf635",
+  "_repo_commit": "d06e377fd7cecda4655e29b6102c94a401b92c49",
   "ancestral_extract": {
     "html_url": "https://github.com/sanger-tol/nf-core-modules/tree/main/modules/sanger-tol/ancestral/extract",
     "errors": 0,
diff --git a/lint_results/modules_warnings.png b/lint_results/modules_warnings.png
diff --git a/lint_results/pipeline-results/readmapping_lint.md b/lint_results/pipeline-results/readmapping_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-02-20T00:09:46.198193411Z
+- Generated: 2026-02-28T00:08:14.576495240Z
 - Nextflow version: 26.01.1-edge
 - Summary: No issues found
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
@@ -284,5 +284,18 @@
     "warnings_high": 4,
     "prints_help_pass": 11,
     "prints_help_fail": 4
+  },
+  {
+    "date": "2026-02-28",
+    "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
@@ -119,7 +119,7 @@
   "readmapping": {
     "full_name": "sanger-tol/readmapping",
     "html_url": "https://github.com/sanger-tol/readmapping",
-    "commit": "7c81160c8328adc95414e226858614e11ad483b3",
+    "commit": "af9c921aa35d087c46b5d8c1940ee3cba4966e45",
     "errors": 0,
     "warnings": 0,
     "parse_error": false,
diff --git a/lint_results/pipelines_warnings.png b/lint_results/pipelines_warnings.png
diff --git a/lint_results/prints-help-results/readmapping_help.txt b/lint_results/prints-help-results/readmapping_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` [mighty_watson] revision: 861ae59bc6
+Launching `./main.nf` [tender_shockley] revision: 861ae59bc6
 
 WARN: Unrecognized config option 'timeline.fields'
 WARN: Unrecognized config option 'validation.defaultIgnoreParams'
@@ -35,16 +35,12 @@ Cloud infrastructure.
   --outfmt                      [string]  Format for output alignment files. Accepts options: "bam" or "cram". [default: cram] 
   --compression                 [string]  Output file compression type. Currently accepts: "none" or "crumble" [default: crumble] 
   --merge_output                [boolean] Merge output alignment files by samples [default: true] 
-  --hifi_adapter_db             [string]  Path to directory or tar.gz archive for pre-built PacBio adapter database. [default: 
-${projectDir}/assets/HiFi_adapter_DB.tar.gz]  
-  --hifi_adapter_yaml           [string]  Path to YAML file containing guide for trimming/filtering PacBio data. See hifi-trimmer docs for 
+  --pacbio_adapter_fasta        [string]  Path to FASTA file contains adapter sequences for PacBio HiFi reads. [default: 
+${projectDir}/assets/HiFi_adapter.fasta]  
+  --pacbio_adapter_yaml         [string]  Path to YAML file containing guide for trimming/filtering PacBio data. See hifi-trimmer docs for 
 details: https://github.com/sanger-tol/hifi-trimmer [default: 
 ${projectDir}/assets/HiFi_adapter.yaml]  
-  --uli_adapter                 [string]  Path to FASTA file containing the PacBio ULI adapter sequence. 
-  --trim_uli_adapter            [boolean] Enable trimming of the PacBio ULI adapter from input reads. [default: false] 
-  --hic_markdup                 [boolean] Enable Hi-C duplicate marking (using 'samtools markdup'). [default: true] 
-  --filter_pacbio               [boolean] Enable filtering and trimming for PacBio reads with hifi-trimmer, if provided reads are already 
-trimmed, please set to false. [default: true]  
+  --pacbio_uli_adapter          [string]  Path to FASTA file containing the PacBio ULI adapter sequence. 
   --email                       [string]  Email address for completion summary. 
 
 Reference genome options
@@ -55,7 +51,10 @@ Reference genome options
 Aligner options
   --short_aligner               [string]  Alignment method to use for short-reads (options are: "minimap2" or "bwamem2"  (accepted: 
 minimap2, bwamem2) [default: bwamem2]  
-  --chunk_size                  [integer] Chunk size for parallel processing of CRAM files, in number of containers [default: 10000] 
+  --long_reads_map_chunk_size   [integer] Chunk size for parallel alignment of long read data, in number of sequences [default: 10000] 
+ 
+  --short_reads_map_chunk_size  [integer] Chunk size for parallel alignment of short read data, in number of cram containers [default: 
+10000]  
 
 Generic options
   --multiqc_title               [string]          MultiQC report title. Printed as page header, used for filename if not otherwise specified. 
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: 2026-02-27T00:12:02.283943+00:00
+- Generated: 2026-02-28T00:08:35.396293+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: 2026-02-27T00:12:02.284106+00:00
+- Generated: 2026-02-28T00:08:35.396487+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: 2026-02-27T00:12:02.284225+00:00
+- Generated: 2026-02-28T00:08:35.396657+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: 2026-02-27T00:12:02.284332+00:00
+- Generated: 2026-02-28T00:08:35.396791+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: 2026-02-27T00:12:02.284478+00:00
+- Generated: 2026-02-28T00:08:35.396887+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: 2026-02-27T00:12:02.284581+00:00
+- Generated: 2026-02-28T00:08:35.396998+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: 2026-02-27T00:12:02.284699+00:00
+- Generated: 2026-02-28T00:08:35.397090+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
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-02-27T00:12:02.284817+00:00
+- Generated: 2026-02-28T00:08:35.397182+00:00
 - Nextflow version: 26.01.1-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/fastx_map_long_reads_lint.md b/lint_results/subworkflow-results/fastx_map_long_reads_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-02-27T00:12:02.284946+00:00
+- Generated: 2026-02-28T00:08:35.397273+00:00
 - Nextflow version: 26.01.1-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/gap_finder_lint.md b/lint_results/subworkflow-results/gap_finder_lint.md
@@ -1,5 +1,21 @@
 # Nextflow lint results
 
-- Generated: 2026-02-27T00:12:02.285074+00:00
+- Generated: 2026-02-28T00:08:35.397363+00:00
 - Nextflow version: 26.01.1-edge
-- Summary: No issues found
+- Summary: 2 warnings
+
+## :warning: Warnings
+
+- Warning: `subworkflows/sanger-tol/gap_finder/main.nf:38:36`: Parameter was not used -- prefix with `_` to suppress warning
+
+  ```nextflow
+          SEQTK_CUTN.out.bed.filter{ meta, file -> val_run_bgzip}
+                                     ^^^^^^^^^^
+  ```
+
+- Warning: `subworkflows/sanger-tol/gap_finder/main.nf:38:42`: Parameter was not used -- prefix with `_` to suppress warning
+
+  ```nextflow
+          SEQTK_CUTN.out.bed.filter{ meta, file -> val_run_bgzip}
+                                           ^^^^^^^^^^
+  ```
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
