Update lint results [skip ci]

github-actions[bot] · github-actions[bot] · commit 7d5c771bc463 · 2026-02-23T00:09:57.000Z
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:** 2026-02-22 00:07:12 UTC
+- **Last updated:** 2026-02-23 00:09:51 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: 2026-02-22T00:06:52.613324+00:00
+- Generated: 2026-02-23T00:09:29.881201+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: 2026-02-22T00:06:52.613466+00:00
+- Generated: 2026-02-23T00:09:29.881367+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: 2026-02-22T00:06:52.613538+00:00
+- Generated: 2026-02-23T00:09:29.881484+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: 2026-02-22T00:06:52.613611+00:00
+- Generated: 2026-02-23T00:09:29.881601+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: 2026-02-22T00:06:52.613671+00:00
+- Generated: 2026-02-23T00:09:29.881715+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: 2026-02-22T00:06:52.613730+00:00
+- Generated: 2026-02-23T00:09:29.881827+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: 2026-02-22T00:06:52.613798+00:00
+- Generated: 2026-02-23T00:09:29.881939+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: 2026-02-22T00:06:52.613859+00:00
+- Generated: 2026-02-23T00:09:29.882108+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: 2026-02-22T00:06:52.613911+00:00
+- Generated: 2026-02-23T00:09:29.882217+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: 2026-02-22T00:06:52.613974+00:00
+- Generated: 2026-02-23T00:09:29.882339+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: 2026-02-22T00:06:52.614066+00:00
+- Generated: 2026-02-23T00:09:29.882451+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: 2026-02-22T00:06:52.614151+00:00
+- Generated: 2026-02-23T00:09:29.882560+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: 2026-02-22T00:06:52.614214+00:00
+- Generated: 2026-02-23T00:09:29.882656+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: 2026-02-22T00:06:52.614274+00:00
+- Generated: 2026-02-23T00:09:29.882773+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: 2026-02-22T00:06:52.614331+00:00
+- Generated: 2026-02-23T00:09:29.882872+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: 2026-02-22T00:06:52.614384+00:00
+- Generated: 2026-02-23T00:09:29.883008+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: 2026-02-22T00:06:52.614434+00:00
+- Generated: 2026-02-23T00:09:29.883120+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: 2026-02-22T00:06:52.614483+00:00
+- Generated: 2026-02-23T00:09:29.883223+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: 2026-02-22T00:06:52.614540+00:00
+- Generated: 2026-02-23T00:09:29.883377+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: 2026-02-22T00:06:52.614601+00:00
+- Generated: 2026-02-23T00:09:29.883509+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: 2026-02-22T00:06:52.614653+00:00
+- Generated: 2026-02-23T00:09:29.883613+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: 2026-02-22T00:06:52.614703+00:00
+- Generated: 2026-02-23T00:09:29.883707+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
@@ -185,5 +185,16 @@
     "warnings_zero": 22,
     "warnings_low": 0,
     "warnings_high": 0
+  },
+  {
+    "date": "2026-02-23",
+    "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
@@ -219,5 +219,18 @@
     "warnings_high": 4,
     "prints_help_pass": 11,
     "prints_help_fail": 4
+  },
+  {
+    "date": "2026-02-23",
+    "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: 2026-02-22T00:06:56.135638+00:00
+- Generated: 2026-02-23T00:09:33.561574+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: 2026-02-22T00:06:56.135780+00:00
+- Generated: 2026-02-23T00:09:33.561725+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: 2026-02-22T00:06:56.135852+00:00
+- Generated: 2026-02-23T00:09:33.561828+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: 2026-02-22T00:06:56.135911+00:00
+- Generated: 2026-02-23T00:09:33.561940+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: 2026-02-22T00:06:56.136002+00:00
+- Generated: 2026-02-23T00:09:33.562078+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: 2026-02-22T00:06:56.136099+00:00
+- Generated: 2026-02-23T00:09:33.562196+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: 2026-02-22T00:06:56.136174+00:00
+- Generated: 2026-02-23T00:09:33.562303+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: 2026-02-22T00:06:56.136242+00:00
+- Generated: 2026-02-23T00:09:33.562401+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: 2026-02-22T00:06:56.136315+00:00
+- Generated: 2026-02-23T00:09:33.562509+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: 2026-02-22T00:06:56.136378+00:00
+- Generated: 2026-02-23T00:09:33.562618+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: 2026-02-22T00:06:56.136434+00:00
+- Generated: 2026-02-23T00:09:33.562720+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: 2026-02-22T00:06:56.136512+00:00
+- Generated: 2026-02-23T00:09:33.562827+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: 2026-02-22T00:06:56.136579+00:00
+- Generated: 2026-02-23T00:09:33.562933+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: 2026-02-22T00:06:56.136633+00:00
+- Generated: 2026-02-23T00:09:33.563083+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
@@ -185,5 +185,16 @@
     "warnings_zero": 14,
     "warnings_low": 0,
     "warnings_high": 0
+  },
+  {
+    "date": "2026-02-23",
+    "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
