Update lint results [skip ci]

github-actions[bot] · github-actions[bot] · commit e51ead54df1d · 2026-02-25T00:11:35.000Z
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:** 2026-02-24 00:10:29 UTC
+- **Last updated:** 2026-02-25 00:11:29 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: 2026-02-24T00:10:09.657574+00:00
+- Generated: 2026-02-25T00:11:10.845874+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: 2026-02-24T00:10:09.657723+00:00
+- Generated: 2026-02-25T00:11:10.846031+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: 2026-02-24T00:10:09.657797+00:00
+- Generated: 2026-02-25T00:11:10.846131+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: 2026-02-24T00:10:09.657859+00:00
+- Generated: 2026-02-25T00:11:10.846297+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: 2026-02-24T00:10:09.657960+00:00
+- Generated: 2026-02-25T00:11:10.846396+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: 2026-02-24T00:10:09.658025+00:00
+- Generated: 2026-02-25T00:11:10.846487+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: 2026-02-24T00:10:09.658080+00:00
+- Generated: 2026-02-25T00:11:10.846605+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: 2026-02-24T00:10:09.658147+00:00
+- Generated: 2026-02-25T00:11:10.846743+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: 2026-02-24T00:10:09.658221+00:00
+- Generated: 2026-02-25T00:11:10.846841+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: 2026-02-24T00:10:09.658283+00:00
+- Generated: 2026-02-25T00:11:10.846995+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: 2026-02-24T00:10:09.658348+00:00
+- Generated: 2026-02-25T00:11:10.847086+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: 2026-02-24T00:10:09.658416+00:00
+- Generated: 2026-02-25T00:11:10.847173+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: 2026-02-24T00:10:09.658483+00:00
+- Generated: 2026-02-25T00:11:10.847309+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: 2026-02-24T00:10:09.658554+00:00
+- Generated: 2026-02-25T00:11:10.847404+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: 2026-02-24T00:10:09.658623+00:00
+- Generated: 2026-02-25T00:11:10.847490+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: 2026-02-24T00:10:09.658679+00:00
+- Generated: 2026-02-25T00:11:10.847643+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: 2026-02-24T00:10:09.658746+00:00
+- Generated: 2026-02-25T00:11:10.847735+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: 2026-02-24T00:10:09.658808+00:00
+- Generated: 2026-02-25T00:11:10.847822+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: 2026-02-24T00:10:09.658924+00:00
+- Generated: 2026-02-25T00:11:10.847966+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: 2026-02-24T00:10:09.659022+00:00
+- Generated: 2026-02-25T00:11:10.848067+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: 2026-02-24T00:10:09.659084+00:00
+- Generated: 2026-02-25T00:11:10.848185+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: 2026-02-24T00:10:09.659145+00:00
+- Generated: 2026-02-25T00:11:10.848345+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
@@ -207,5 +207,16 @@
     "warnings_zero": 22,
     "warnings_low": 0,
     "warnings_high": 0
+  },
+  {
+    "date": "2026-02-25",
+    "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
@@ -245,5 +245,18 @@
     "warnings_high": 4,
     "prints_help_pass": 11,
     "prints_help_fail": 4
+  },
+  {
+    "date": "2026-02-25",
+    "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_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: 2026-02-24T00:10:13.229269+00:00
+- Generated: 2026-02-25T00:11:14.480190+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: 2026-02-24T00:10:13.229410+00:00
+- Generated: 2026-02-25T00:11:14.480355+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: 2026-02-24T00:10:13.229495+00:00
+- Generated: 2026-02-25T00:11:14.480456+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: 2026-02-24T00:10:13.229565+00:00
+- Generated: 2026-02-25T00:11:14.480548+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: 2026-02-24T00:10:13.229626+00:00
+- Generated: 2026-02-25T00:11:14.480638+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: 2026-02-24T00:10:13.229697+00:00
+- Generated: 2026-02-25T00:11:14.480726+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: 2026-02-24T00:10:13.229765+00:00
+- Generated: 2026-02-25T00:11:14.480812+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: 2026-02-24T00:10:13.229821+00:00
+- Generated: 2026-02-25T00:11:14.480897+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: 2026-02-24T00:10:13.229933+00:00
+- Generated: 2026-02-25T00:11:14.480982+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: 2026-02-24T00:10:13.230001+00:00
+- Generated: 2026-02-25T00:11:14.481071+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: 2026-02-24T00:10:13.230065+00:00
+- Generated: 2026-02-25T00:11:14.481157+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: 2026-02-24T00:10:13.230126+00:00
+- Generated: 2026-02-25T00:11:14.481278+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: 2026-02-24T00:10:13.230187+00:00
+- Generated: 2026-02-25T00:11:14.481372+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: 2026-02-24T00:10:13.230249+00:00
+- Generated: 2026-02-25T00:11:14.481458+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
@@ -207,5 +207,16 @@
     "warnings_zero": 14,
     "warnings_low": 0,
     "warnings_high": 0
+  },
+  {
+    "date": "2026-02-25",
+    "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
