Update lint results [skip ci]

Author: github-actions[bot]

README.md

@@ -11,12 +11,12 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
 > 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:** 2026-05-27 00:44:52 UTC
+- **Last updated:** 2026-05-28 00:41:51 UTC
 - **Nextflow version:** 26.04.2
 
 ## Pipelines
 
-- **Total:** 0 parse errors, 1728 errors, 7569 warnings across 137 pipelines
+- **Total:** 0 parse errors, 1728 errors, 7558 warnings across 137 pipelines
 - **Zero errors:** 73 pipelines (53.3%)
 
 |                    Errors                    |                     Warnings                     |
@@ -92,7 +92,7 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
 | :x: [dualrnaseq](https://github.com/nf-core/dualrnaseq)                                        |     No      |      2 |       48 |      -      |        [View](lint_results/pipeline-results/dualrnaseq_lint.md)         |                                    -                                     |
 | :x: [cellpainting](https://github.com/nf-core/cellpainting)                                    |     No      |      2 |       10 |      -      |       [View](lint_results/pipeline-results/cellpainting_lint.md)        |                                    -                                     |
 | :x: [scnanoseq](https://github.com/nf-core/scnanoseq)                                          |     No      |      1 |        5 |      -      |         [View](lint_results/pipeline-results/scnanoseq_lint.md)         |                                    -                                     |
-| :white_check_mark: [sarek](https://github.com/nf-core/sarek)                                   |     No      |      0 |      651 |     Yes     |           [View](lint_results/pipeline-results/sarek_lint.md)           |         [View](lint_results/prints-help-results/sarek_help.txt)          |
+| :white_check_mark: [sarek](https://github.com/nf-core/sarek)                                   |     No      |      0 |      617 |     Yes     |           [View](lint_results/pipeline-results/sarek_lint.md)           |         [View](lint_results/prints-help-results/sarek_help.txt)          |
 | :x: [longraredisease](https://github.com/nf-core/longraredisease)                              |     No      |      0 |      182 |     No      |      [View](lint_results/pipeline-results/longraredisease_lint.md)      |    [View](lint_results/prints-help-results/longraredisease_help.txt)     |
 | :white_check_mark: [atacseq](https://github.com/nf-core/atacseq)                               |     No      |      0 |      161 |     Yes     |          [View](lint_results/pipeline-results/atacseq_lint.md)          |        [View](lint_results/prints-help-results/atacseq_help.txt)         |
 | :x: [cutandrun](https://github.com/nf-core/cutandrun)                                          |     No      |      0 |      156 |     No      |         [View](lint_results/pipeline-results/cutandrun_lint.md)         |       [View](lint_results/prints-help-results/cutandrun_help.txt)        |
@@ -102,8 +102,8 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
 | :white_check_mark: [differentialabundance](https://github.com/nf-core/differentialabundance)   |     No      |      0 |      107 |     Yes     |   [View](lint_results/pipeline-results/differentialabundance_lint.md)   | [View](lint_results/prints-help-results/differentialabundance_help.txt)  |
 | :white_check_mark: [taxprofiler](https://github.com/nf-core/taxprofiler)                       |     No      |      0 |       94 |     Yes     |        [View](lint_results/pipeline-results/taxprofiler_lint.md)        |      [View](lint_results/prints-help-results/taxprofiler_help.txt)       |
 | :white_check_mark: [funcscan](https://github.com/nf-core/funcscan)                             |     No      |      0 |       80 |     Yes     |         [View](lint_results/pipeline-results/funcscan_lint.md)          |        [View](lint_results/prints-help-results/funcscan_help.txt)        |
+| :white_check_mark: [chipseq](https://github.com/nf-core/chipseq)                               |     No      |      0 |       76 |     Yes     |          [View](lint_results/pipeline-results/chipseq_lint.md)          |        [View](lint_results/prints-help-results/chipseq_help.txt)         |
 | :x: [deepmutscan](https://github.com/nf-core/deepmutscan)                                      |     No      |      0 |       76 |     No      |        [View](lint_results/pipeline-results/deepmutscan_lint.md)        |      [View](lint_results/prints-help-results/deepmutscan_help.txt)       |
-| :white_check_mark: [chipseq](https://github.com/nf-core/chipseq)                               |     No      |      0 |       70 |     Yes     |          [View](lint_results/pipeline-results/chipseq_lint.md)          |        [View](lint_results/prints-help-results/chipseq_help.txt)         |
 | :x: [methylong](https://github.com/nf-core/methylong)                                          |     No      |      0 |       66 |     No      |         [View](lint_results/pipeline-results/methylong_lint.md)         |       [View](lint_results/prints-help-results/methylong_help.txt)        |
 | :white_check_mark: [abotyper](https://github.com/nf-core/abotyper)                             |     No      |      0 |       65 |     Yes     |         [View](lint_results/pipeline-results/abotyper_lint.md)          |        [View](lint_results/prints-help-results/abotyper_help.txt)        |
 | :white_check_mark: [scrnaseq](https://github.com/nf-core/scrnaseq)                             |     No      |      0 |       60 |     Yes     |         [View](lint_results/pipeline-results/scrnaseq_lint.md)          |        [View](lint_results/prints-help-results/scrnaseq_help.txt)        |
@@ -132,8 +132,10 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
 | :x: [genephylomodeler](https://github.com/nf-core/genephylomodeler)                            |     No      |      0 |       13 |     No      |     [View](lint_results/pipeline-results/genephylomodeler_lint.md)      |    [View](lint_results/prints-help-results/genephylomodeler_help.txt)    |
 | :white_check_mark: [raredisease](https://github.com/nf-core/raredisease)                       |     No      |      0 |       13 |     Yes     |        [View](lint_results/pipeline-results/raredisease_lint.md)        |      [View](lint_results/prints-help-results/raredisease_help.txt)       |
 | :white_check_mark: [seqsubmit](https://github.com/nf-core/seqsubmit)                           |     No      |      0 |       12 |     Yes     |         [View](lint_results/pipeline-results/seqsubmit_lint.md)         |       [View](lint_results/prints-help-results/seqsubmit_help.txt)        |
+| :white_check_mark: [viralmetagenome](https://github.com/nf-core/viralmetagenome)               |     No      |      0 |       11 |     Yes     |      [View](lint_results/pipeline-results/viralmetagenome_lint.md)      |    [View](lint_results/prints-help-results/viralmetagenome_help.txt)     |
 | :white_check_mark: [genomeqc](https://github.com/nf-core/genomeqc)                             |     No      |      0 |       10 |     Yes     |         [View](lint_results/pipeline-results/genomeqc_lint.md)          |        [View](lint_results/prints-help-results/genomeqc_help.txt)        |
 | :white_check_mark: [genomicrelatedness](https://github.com/nf-core/genomicrelatedness)         |     No      |      0 |       10 |     Yes     |    [View](lint_results/pipeline-results/genomicrelatedness_lint.md)     |   [View](lint_results/prints-help-results/genomicrelatedness_help.txt)   |
+| :x: [spatialaxe](https://github.com/nf-core/spatialaxe)                                        |     No      |      0 |       10 |     No      |        [View](lint_results/pipeline-results/spatialaxe_lint.md)         |       [View](lint_results/prints-help-results/spatialaxe_help.txt)       |
 | :white_check_mark: [tfactivity](https://github.com/nf-core/tfactivity)                         |     No      |      0 |       10 |     Yes     |        [View](lint_results/pipeline-results/tfactivity_lint.md)         |       [View](lint_results/prints-help-results/tfactivity_help.txt)       |
 | :white_check_mark: [fetchngs](https://github.com/nf-core/fetchngs)                             |     No      |      0 |        9 |     Yes     |         [View](lint_results/pipeline-results/fetchngs_lint.md)          |        [View](lint_results/prints-help-results/fetchngs_help.txt)        |
 | :x: [fastquorum](https://github.com/nf-core/fastquorum)                                        |     No      |      0 |        8 |     No      |        [View](lint_results/pipeline-results/fastquorum_lint.md)         |       [View](lint_results/prints-help-results/fastquorum_help.txt)       |
@@ -146,9 +148,8 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
 | :white_check_mark: [magmap](https://github.com/nf-core/magmap)                                 |     No      |      0 |        5 |     Yes     |          [View](lint_results/pipeline-results/magmap_lint.md)           |         [View](lint_results/prints-help-results/magmap_help.txt)         |
 | :white_check_mark: [epitopeprediction](https://github.com/nf-core/epitopeprediction)           |     No      |      0 |        4 |     Yes     |     [View](lint_results/pipeline-results/epitopeprediction_lint.md)     |   [View](lint_results/prints-help-results/epitopeprediction_help.txt)    |
 | :x: [ncrnannotator](https://github.com/nf-core/ncrnannotator)                                  |     No      |      0 |        4 |     No      |       [View](lint_results/pipeline-results/ncrnannotator_lint.md)       |     [View](lint_results/prints-help-results/ncrnannotator_help.txt)      |
-| :x: [spatialxe](https://github.com/nf-core/spatialxe)                                          |     No      |      0 |        4 |     No      |         [View](lint_results/pipeline-results/spatialxe_lint.md)         |       [View](lint_results/prints-help-results/spatialxe_help.txt)        |
 | :white_check_mark: [proteinfamilies](https://github.com/nf-core/proteinfamilies)               |     No      |      0 |        3 |     Yes     |      [View](lint_results/pipeline-results/proteinfamilies_lint.md)      |    [View](lint_results/prints-help-results/proteinfamilies_help.txt)     |
-| :white_check_mark: [viralmetagenome](https://github.com/nf-core/viralmetagenome)               |     No      |      0 |        3 |     Yes     |      [View](lint_results/pipeline-results/viralmetagenome_lint.md)      |    [View](lint_results/prints-help-results/viralmetagenome_help.txt)     |
+| :white_check_mark: [rnavar](https://github.com/nf-core/rnavar)                                 |     No      |      0 |        3 |     Yes     |          [View](lint_results/pipeline-results/rnavar_lint.md)           |         [View](lint_results/prints-help-results/rnavar_help.txt)         |
 | :white_check_mark: [hlatyping](https://github.com/nf-core/hlatyping)                           |     No      |      0 |        2 |     Yes     |         [View](lint_results/pipeline-results/hlatyping_lint.md)         |       [View](lint_results/prints-help-results/hlatyping_help.txt)        |
 | :x: [ribomsqc](https://github.com/nf-core/ribomsqc)                                            |     No      |      0 |        2 |     No      |         [View](lint_results/pipeline-results/ribomsqc_lint.md)          |        [View](lint_results/prints-help-results/ribomsqc_help.txt)        |
 | :white_check_mark: [spatialvi](https://github.com/nf-core/spatialvi)                           |     No      |      0 |        2 |     Yes     |         [View](lint_results/pipeline-results/spatialvi_lint.md)         |       [View](lint_results/prints-help-results/spatialvi_help.txt)        |
@@ -163,15 +164,14 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
 | :white_check_mark: [nanostring](https://github.com/nf-core/nanostring)                         |     No      |      0 |        0 |     Yes     |        [View](lint_results/pipeline-results/nanostring_lint.md)         |       [View](lint_results/prints-help-results/nanostring_help.txt)       |
 | :white_check_mark: [proteinannotator](https://github.com/nf-core/proteinannotator)             |     No      |      0 |        0 |     Yes     |     [View](lint_results/pipeline-results/proteinannotator_lint.md)      |    [View](lint_results/prints-help-results/proteinannotator_help.txt)    |
 | :white_check_mark: [rnaseq](https://github.com/nf-core/rnaseq)                                 |     No      |      0 |        0 |     Yes     |          [View](lint_results/pipeline-results/rnaseq_lint.md)           |         [View](lint_results/prints-help-results/rnaseq_help.txt)         |
-| :white_check_mark: [rnavar](https://github.com/nf-core/rnavar)                                 |     No      |      0 |        0 |     Yes     |          [View](lint_results/pipeline-results/rnavar_lint.md)           |         [View](lint_results/prints-help-results/rnavar_help.txt)         |
 | :white_check_mark: [seqinspector](https://github.com/nf-core/seqinspector)                     |     No      |      0 |        0 |     Yes     |       [View](lint_results/pipeline-results/seqinspector_lint.md)        |      [View](lint_results/prints-help-results/seqinspector_help.txt)      |
 
 </details>
 
 ## Modules
 
-- **Total:** 0 parse errors, 0 errors, 3 warnings across 1850 modules
-- **Zero errors:** 1850 modules (100.0%)
+- **Total:** 0 parse errors, 0 errors, 3 warnings across 1853 modules
+- **Zero errors:** 1853 modules (100.0%)
 
 |                   Errors                   |                    Warnings                    |
 | :----------------------------------------: | :--------------------------------------------: |
@@ -183,7 +183,7 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
 | Module | Parse Error | Errors | Warnings | Lint Output |
 | ------ | :---------: | -----: | -------: | :---------: |
 
-_Modules with zero errors are not shown above (1850 modules). They may still have warnings. See the [modules results directory](lint_results/module-results/) for all lint outputs._
+_Modules with zero errors are not shown above (1853 modules). They may still have warnings. See the [modules results directory](lint_results/module-results/) for all lint outputs._
 
 </details>
 

lint_results/module-results/abacas_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-27T00:44:25.693162+00:00
+- Generated: 2026-05-28T00:41:17.298835+00:00
 - Nextflow version: 26.04.2
 - Summary: No issues found

lint_results/module-results/abra2_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-27T00:44:25.693332+00:00
+- Generated: 2026-05-28T00:41:17.299034+00:00
 - Nextflow version: 26.04.2
 - Summary: No issues found

lint_results/module-results/abricate_run_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-27T00:44:25.693443+00:00
+- Generated: 2026-05-28T00:41:17.299179+00:00
 - Nextflow version: 26.04.2
 - Summary: No issues found

lint_results/module-results/abricate_summary_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-27T00:44:25.693547+00:00
+- Generated: 2026-05-28T00:41:17.299344+00:00
 - Nextflow version: 26.04.2
 - Summary: No issues found

lint_results/module-results/abritamr_run_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-27T00:44:25.693684+00:00
+- Generated: 2026-05-28T00:41:17.299485+00:00
 - Nextflow version: 26.04.2
 - Summary: No issues found

lint_results/module-results/abyss_abysspe_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-27T00:44:25.693789+00:00
+- Generated: 2026-05-28T00:41:17.299618+00:00
 - Nextflow version: 26.04.2
 - Summary: No issues found

lint_results/module-results/adapterremoval_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-27T00:44:25.693887+00:00
+- Generated: 2026-05-28T00:41:17.299749+00:00
 - Nextflow version: 26.04.2
 - Summary: No issues found

lint_results/module-results/adapterremovalfixprefix_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-27T00:44:25.693984+00:00
+- Generated: 2026-05-28T00:41:17.299878+00:00
 - Nextflow version: 26.04.2
 - Summary: No issues found

lint_results/module-results/admixture_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-27T00:44:25.694084+00:00
+- Generated: 2026-05-28T00:41:17.300006+00:00
 - Nextflow version: 26.04.2
 - Summary: No issues found