Update lint results [skip ci]

github-actions[bot] · github-actions[bot] · commit 5073077a5a5c · 2026-03-21T00:08:07.000Z
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:** 2026-03-20 17:32:32 UTC
+- **Last updated:** 2026-03-21 00:07:59 UTC
 - **Nextflow version:** 26.03.0-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: 2026-03-20T17:32:07.237867+00:00
+- Generated: 2026-03-21T00:07:37.047818+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.238026+00:00
+- Generated: 2026-03-21T00:07:37.048007+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/asmstats_lint.md b/lint_results/module-results/asmstats_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:07.238133+00:00
+- Generated: 2026-03-21T00:07:37.048147+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.238233+00:00
+- Generated: 2026-03-21T00:07:37.048296+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.238364+00:00
+- Generated: 2026-03-21T00:07:37.048465+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/bgziptabix_lint.md b/lint_results/module-results/bgziptabix_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:07.238476+00:00
+- Generated: 2026-03-21T00:07:37.048589+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.238573+00:00
+- Generated: 2026-03-21T00:07:37.050443+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.238666+00:00
+- Generated: 2026-03-21T00:07:37.050552+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.238758+00:00
+- Generated: 2026-03-21T00:07:37.050663+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/contactbed_lint.md b/lint_results/module-results/contactbed_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:07.238905+00:00
+- Generated: 2026-03-21T00:07:37.050761+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.238998+00:00
+- Generated: 2026-03-21T00:07:37.050854+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.239089+00:00
+- Generated: 2026-03-21T00:07:37.050951+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.239180+00:00
+- Generated: 2026-03-21T00:07:37.051059+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.239271+00:00
+- Generated: 2026-03-21T00:07:37.051165+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.239359+00:00
+- Generated: 2026-03-21T00:07:37.051273+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.239448+00:00
+- Generated: 2026-03-21T00:07:37.051407+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.239538+00:00
+- Generated: 2026-03-21T00:07:37.051513+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/generatecontactsindex_lint.md b/lint_results/module-results/generatecontactsindex_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:07.239626+00:00
+- Generated: 2026-03-21T00:07:37.051606+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/gnk_fastasort_lint.md b/lint_results/module-results/gnk_fastasort_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:07.239716+00:00
+- Generated: 2026-03-21T00:07:37.051696+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/hifiasm_lint.md b/lint_results/module-results/hifiasm_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:07.239845+00:00
+- Generated: 2026-03-21T00:07:37.051786+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.239949+00:00
+- Generated: 2026-03-21T00:07:37.051898+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.240058+00:00
+- Generated: 2026-03-21T00:07:37.052010+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.240174+00:00
+- Generated: 2026-03-21T00:07:37.052105+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.240278+00:00
+- Generated: 2026-03-21T00:07:37.052197+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/pretextannotate_lint.md b/lint_results/module-results/pretextannotate_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:07.240403+00:00
+- Generated: 2026-03-21T00:07:37.052320+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/module-results/restructurebuscodir_lint.md b/lint_results/module-results/restructurebuscodir_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:07.240506+00:00
+- Generated: 2026-03-21T00:07:37.052445+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.240598+00:00
+- Generated: 2026-03-21T00:07:37.052539+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.240712+00:00
+- Generated: 2026-03-21T00:07:37.052630+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.240876+00:00
+- Generated: 2026-03-21T00:07:37.052720+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.240995+00:00
+- Generated: 2026-03-21T00:07:37.052834+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.241108+00:00
+- Generated: 2026-03-21T00:07:37.052943+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:07.241233+00:00
+- Generated: 2026-03-21T00:07:37.053034+00:00
 - Nextflow version: 26.03.0-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
@@ -475,5 +475,18 @@
     "warnings_high": 0,
     "meta_with_topic_versions": 32,
     "meta_without_topic_versions": 0
+  },
+  {
+    "date": "2026-03-21",
+    "total": 32,
+    "parse_errors": 0,
+    "errors_zero": 32,
+    "errors_low": 0,
+    "errors_high": 0,
+    "warnings_zero": 32,
+    "warnings_low": 0,
+    "warnings_high": 0,
+    "meta_with_topic_versions": 32,
+    "meta_without_topic_versions": 0
   }
 ]
diff --git a/lint_results/modules_topic_versions.png b/lint_results/modules_topic_versions.png
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
@@ -557,5 +557,18 @@
     "warnings_high": 2,
     "prints_help_pass": 11,
     "prints_help_fail": 6
+  },
+  {
+    "date": "2026-03-21",
+    "total": 19,
+    "parse_errors": 0,
+    "errors_zero": 17,
+    "errors_low": 2,
+    "errors_high": 0,
+    "warnings_zero": 10,
+    "warnings_low": 7,
+    "warnings_high": 2,
+    "prints_help_pass": 11,
+    "prints_help_fail": 6
   }
 ]
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: 2026-03-20T17:32:11.389714+00:00
+- Generated: 2026-03-21T00:07:41.120119+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:11.389891+00:00
+- Generated: 2026-03-21T00:07:41.120277+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:11.389997+00:00
+- Generated: 2026-03-21T00:07:41.120414+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:11.390094+00:00
+- Generated: 2026-03-21T00:07:41.120543+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:11.390227+00:00
+- Generated: 2026-03-21T00:07:41.120661+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:11.391573+00:00
+- Generated: 2026-03-21T00:07:41.120764+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:11.391674+00:00
+- Generated: 2026-03-21T00:07:41.120886+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:11.391790+00:00
+- Generated: 2026-03-21T00:07:41.120999+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:11.391896+00:00
+- Generated: 2026-03-21T00:07:41.121115+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:11.391990+00:00
+- Generated: 2026-03-21T00:07:41.121226+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/feature_density_lint.md b/lint_results/subworkflow-results/feature_density_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:11.392083+00:00
+- Generated: 2026-03-21T00:07:41.121337+00:00
 - Nextflow version: 26.03.0-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
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:11.392175+00:00
+- Generated: 2026-03-21T00:07:41.121498+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:11.392268+00:00
+- Generated: 2026-03-21T00:07:41.121597+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/get_blobtk_plots_lint.md b/lint_results/subworkflow-results/get_blobtk_plots_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:11.392360+00:00
+- Generated: 2026-03-21T00:07:41.121725+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:11.392454+00:00
+- Generated: 2026-03-21T00:07:41.121823+00:00
 - Nextflow version: 26.03.0-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: 2026-03-20T17:32:11.392544+00:00
+- Generated: 2026-03-21T00:07:41.121940+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/repeat_density_lint.md b/lint_results/subworkflow-results/repeat_density_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:11.392633+00:00
+- Generated: 2026-03-21T00:07:41.122039+00:00
 - Nextflow version: 26.03.0-edge
 - Summary: No issues found
diff --git a/lint_results/subworkflow-results/repeat_masking_lint.md b/lint_results/subworkflow-results/repeat_masking_lint.md
@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-03-20T17:32:11.392724+00:00
+- Generated: 2026-03-21T00:07:41.122132+00:00
 - Nextflow version: 26.03.0-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
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_warnings.png b/lint_results/subworkflows_warnings.png
