Update lint results [skip ci]

github-actions[bot] · github-actions[bot] · commit ab72732c1b97 · 2026-02-14T00:09:09.000Z
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:** 2026-02-13 00:10:54 UTC
+- **Last updated:** 2026-02-14 00:08:58 UTC
 - **Nextflow version:** 26.01.1-edge
 
 ## Pipelines
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: 2026-02-13T00:10:31.735840+00:00
+- Generated: 2026-02-14T00:08:43.677741+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: 2026-02-13T00:10:31.736002+00:00
+- Generated: 2026-02-14T00:08:43.677903+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: 2026-02-13T00:10:31.736109+00:00
+- Generated: 2026-02-14T00:08:43.678063+00:00
 - Nextflow version: 26.01.1-edge
-- Summary: No issues found
+- 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: 2026-02-13T00:10:31.736203+00:00
+- Generated: 2026-02-14T00:08:43.678185+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: 2026-02-13T00:10:31.736299+00:00
+- Generated: 2026-02-14T00:08:43.678299+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: 2026-02-13T00:10:31.736392+00:00
+- Generated: 2026-02-14T00:08:43.678400+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: 2026-02-13T00:10:31.736483+00:00
+- Generated: 2026-02-14T00:08:43.678525+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: 2026-02-13T00:10:31.736616+00:00
+- Generated: 2026-02-14T00:08:43.678642+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: 2026-02-13T00:10:31.736720+00:00
+- Generated: 2026-02-14T00:08:43.678755+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: 2026-02-13T00:10:31.736815+00:00
+- Generated: 2026-02-14T00:08:43.678865+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: 2026-02-13T00:10:31.736907+00:00
+- Generated: 2026-02-14T00:08:43.679012+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: 2026-02-13T00:10:31.736999+00:00
+- Generated: 2026-02-14T00:08:43.679136+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: 2026-02-13T00:10:31.737092+00:00
+- Generated: 2026-02-14T00:08:43.679249+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: 2026-02-13T00:10:31.737182+00:00
+- Generated: 2026-02-14T00:08:43.679348+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: 2026-02-13T00:10:31.737272+00:00
+- Generated: 2026-02-14T00:08:43.679468+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: 2026-02-13T00:10:31.737424+00:00
+- Generated: 2026-02-14T00:08:43.679577+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: 2026-02-13T00:10:31.738811+00:00
+- Generated: 2026-02-14T00:08:43.679688+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: 2026-02-13T00:10:31.738938+00:00
+- Generated: 2026-02-14T00:08:43.679801+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: 2026-02-13T00:10:31.739065+00:00
+- Generated: 2026-02-14T00:08:43.679911+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: 2026-02-13T00:10:31.739184+00:00
+- Generated: 2026-02-14T00:08:43.680046+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: 2026-02-13T00:10:31.739304+00:00
+- Generated: 2026-02-14T00:08:43.680157+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: 2026-02-13T00:10:31.739432+00:00
+- Generated: 2026-02-14T00:08:43.680267+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
@@ -86,5 +86,16 @@
     "warnings_zero": 22,
     "warnings_low": 0,
     "warnings_high": 0
+  },
+  {
+    "date": "2026-02-14",
+    "total": 22,
+    "parse_errors": 0,
+    "errors_zero": 22,
+    "errors_low": 0,
+    "errors_high": 0,
+    "warnings_zero": 22,
+    "warnings_low": 0,
+    "warnings_high": 0
   }
 ]
diff --git a/lint_results/modules_warnings.png b/lint_results/modules_warnings.png
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
@@ -102,5 +102,18 @@
     "warnings_high": 5,
     "prints_help_pass": 11,
     "prints_help_fail": 3
+  },
+  {
+    "date": "2026-02-14",
+    "total": 19,
+    "parse_errors": 0,
+    "errors_zero": 14,
+    "errors_low": 2,
+    "errors_high": 3,
+    "warnings_zero": 9,
+    "warnings_low": 5,
+    "warnings_high": 5,
+    "prints_help_pass": 11,
+    "prints_help_fail": 3
   }
 ]
diff --git a/lint_results/pipelines_warnings.png b/lint_results/pipelines_warnings.png
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: 2026-02-13T00:10:35.406351+00:00
+- Generated: 2026-02-14T00:08:47.430807+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: 2026-02-13T00:10:35.406501+00:00
+- Generated: 2026-02-14T00:08:47.430998+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: 2026-02-13T00:10:35.406638+00:00
+- Generated: 2026-02-14T00:08:47.431114+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: 2026-02-13T00:10:35.406743+00:00
+- Generated: 2026-02-14T00:08:47.431225+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: 2026-02-13T00:10:35.406840+00:00
+- Generated: 2026-02-14T00:08:47.431325+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: 2026-02-13T00:10:35.406934+00:00
+- Generated: 2026-02-14T00:08:47.431422+00:00
 - Nextflow version: 26.01.1-edge
-- Summary: No issues found
+- 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: 2026-02-13T00:10:35.407024+00:00
+- Generated: 2026-02-14T00:08:47.431521+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: 2026-02-13T00:10:35.407123+00:00
+- Generated: 2026-02-14T00:08:47.431616+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: 2026-02-13T00:10:35.407215+00:00
+- Generated: 2026-02-14T00:08:47.431713+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 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-02-13T00:10:35.407307+00:00
+- Generated: 2026-02-14T00:08:47.431808+00:00
 - Nextflow version: 26.01.1-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/genome_statistics_lint.md b/lint_results/subworkflow-results/genome_statistics_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-02-13T00:10:35.407397+00:00
+- Generated: 2026-02-14T00:08:47.431903+00:00
 - Nextflow version: 26.01.1-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/pacbio_preprocess_lint.md b/lint_results/subworkflow-results/pacbio_preprocess_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-02-13T00:10:35.407487+00:00
+- Generated: 2026-02-14T00:08:47.432019+00:00
 - Nextflow version: 26.01.1-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/pairs_create_contact_maps_lint.md b/lint_results/subworkflow-results/pairs_create_contact_maps_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-02-13T00:10:35.407640+00:00
+- Generated: 2026-02-14T00:08:47.432115+00:00
 - Nextflow version: 26.01.1-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/telo_finder_lint.md b/lint_results/subworkflow-results/telo_finder_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-02-13T00:10:35.407746+00:00
+- Generated: 2026-02-14T00:08:47.432209+00:00
 - Nextflow version: 26.01.1-edge
 - Summary: No issues found
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
@@ -86,5 +86,16 @@
     "warnings_zero": 14,
     "warnings_low": 0,
     "warnings_high": 0
+  },
+  {
+    "date": "2026-02-14",
+    "total": 14,
+    "parse_errors": 0,
+    "errors_zero": 14,
+    "errors_low": 0,
+    "errors_high": 0,
+    "warnings_zero": 14,
+    "warnings_low": 0,
+    "warnings_high": 0
   }
 ]
diff --git a/lint_results/subworkflows_warnings.png b/lint_results/subworkflows_warnings.png
