Update lint results [skip ci]

github-actions[bot] · github-actions[bot] · commit 4bbaeafb0f80 · 2026-03-02T00:06:36.000Z
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:** 2026-03-01 00:09:41 UTC
+- **Last updated:** 2026-03-02 00:06:30 UTC
 - **Nextflow version:** 26.02.0-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: 2026-03-01T00:09:22.026257+00:00
+- Generated: 2026-03-02T00:06:10.080220+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.026424+00:00
+- Generated: 2026-03-02T00:06:10.080383+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.026549+00:00
+- Generated: 2026-03-02T00:06:10.080504+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.026656+00:00
+- Generated: 2026-03-02T00:06:10.080645+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.026784+00:00
+- Generated: 2026-03-02T00:06:10.080771+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.026901+00:00
+- Generated: 2026-03-02T00:06:10.080898+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.027002+00:00
+- Generated: 2026-03-02T00:06:10.080999+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.027149+00:00
+- Generated: 2026-03-02T00:06:10.081138+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.027265+00:00
+- Generated: 2026-03-02T00:06:10.081334+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.027379+00:00
+- Generated: 2026-03-02T00:06:10.081458+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.027492+00:00
+- Generated: 2026-03-02T00:06:10.081554+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.027604+00:00
+- Generated: 2026-03-02T00:06:10.081687+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.027712+00:00
+- Generated: 2026-03-02T00:06:10.081809+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.027829+00:00
+- Generated: 2026-03-02T00:06:10.081945+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.027940+00:00
+- Generated: 2026-03-02T00:06:10.082062+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.028033+00:00
+- Generated: 2026-03-02T00:06:10.082222+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.028149+00:00
+- Generated: 2026-03-02T00:06:10.082339+00:00
 - Nextflow version: 26.02.0-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
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-01T00:09:22.028239+00:00
+- Generated: 2026-03-02T00:06:10.082443+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.041533+00:00
+- Generated: 2026-03-02T00:06:10.082549+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.041693+00:00
+- Generated: 2026-03-02T00:06:10.082638+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.041825+00:00
+- Generated: 2026-03-02T00:06:10.082755+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.041934+00:00
+- Generated: 2026-03-02T00:06:10.082858+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.042061+00:00
+- Generated: 2026-03-02T00:06:10.082947+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:22.042208+00:00
+- Generated: 2026-03-02T00:06:10.083047+00:00
 - Nextflow version: 26.02.0-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
@@ -262,5 +262,16 @@
     "warnings_zero": 24,
     "warnings_low": 0,
     "warnings_high": 0
+  },
+  {
+    "date": "2026-03-02",
+    "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_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
@@ -310,5 +310,18 @@
     "warnings_high": 4,
     "prints_help_pass": 11,
     "prints_help_fail": 4
+  },
+  {
+    "date": "2026-03-02",
+    "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: 2026-03-01T00:09:25.932871+00:00
+- Generated: 2026-03-02T00:06:13.905165+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:25.933031+00:00
+- Generated: 2026-03-02T00:06:13.905321+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:25.933184+00:00
+- Generated: 2026-03-02T00:06:13.905422+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:25.933299+00:00
+- Generated: 2026-03-02T00:06:13.905544+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:25.933426+00:00
+- Generated: 2026-03-02T00:06:13.905670+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:25.933542+00:00
+- Generated: 2026-03-02T00:06:13.905785+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:25.933665+00:00
+- Generated: 2026-03-02T00:06:13.905925+00:00
 - Nextflow version: 26.02.0-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/fasta_compress_index_lint.md b/lint_results/subworkflow-results/fasta_compress_index_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-01T00:09:25.933784+00:00
+- Generated: 2026-03-02T00:06:13.906047+00:00
 - Nextflow version: 26.02.0-edge
-- Summary: No issues found
+- 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: 2026-03-01T00:09:25.933893+00:00
+- Generated: 2026-03-02T00:06:13.906227+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:25.933998+00:00
+- Generated: 2026-03-02T00:06:13.906360+00:00
 - Nextflow version: 26.02.0-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
@@ -1,6 +1,6 @@
 # Nextflow lint results
 
-- Generated: 2026-03-01T00:09:25.934139+00:00
+- Generated: 2026-03-02T00:06:13.906479+00:00
 - Nextflow version: 26.02.0-edge
 - Summary: 2 warnings
 
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: 2026-03-01T00:09:25.934408+00:00
+- Generated: 2026-03-02T00:06:13.906753+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:25.934526+00:00
+- Generated: 2026-03-02T00:06:13.906870+00:00
 - Nextflow version: 26.02.0-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: 2026-03-01T00:09:25.934645+00:00
+- Generated: 2026-03-02T00:06:13.906971+00:00
 - Nextflow version: 26.02.0-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/soft_masked_fasta_repeats_lint.md b/lint_results/subworkflow-results/soft_masked_fasta_repeats_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-01T00:09:25.934761+00:00
+- Generated: 2026-03-02T00:06:13.907091+00:00
 - Nextflow version: 26.02.0-edge
-- Summary: No issues found
+- 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: 2026-03-01T00:09:25.934854+00:00
+- Generated: 2026-03-02T00:06:13.907261+00:00
 - Nextflow version: 26.02.0-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
@@ -262,5 +262,16 @@
     "warnings_zero": 15,
     "warnings_low": 1,
     "warnings_high": 0
+  },
+  {
+    "date": "2026-03-02",
+    "total": 16,
+    "parse_errors": 0,
+    "errors_zero": 16,
+    "errors_low": 0,
+    "errors_high": 0,
+    "warnings_zero": 15,
+    "warnings_low": 1,
+    "warnings_high": 0
   }
 ]
diff --git a/lint_results/subworkflows_warnings.png b/lint_results/subworkflows_warnings.png
