Update lint results [skip ci]

Author: github-actions[bot]

README.md

@@ -11,13 +11,13 @@ 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:** 2026-05-28 00:41:51 UTC
-- **Nextflow version:** 26.04.2
+- **Last updated:** 2026-05-29 00:46:03 UTC
+- **Nextflow version:** 26.04.3
 
 ## Pipelines
 
-- **Total:** 0 parse errors, 1728 errors, 7558 warnings across 137 pipelines
-- **Zero errors:** 73 pipelines (53.3%)
+- **Total:** 0 parse errors, 1727 errors, 7573 warnings across 137 pipelines
+- **Zero errors:** 74 pipelines (54.0%)
 
 |                    Errors                    |                     Warnings                     |
 | :------------------------------------------: | :----------------------------------------------: |
@@ -91,8 +91,7 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
 | :x: [reportho](https://github.com/nf-core/reportho)                                            |     No      |      2 |       90 |      -      |         [View](lint_results/pipeline-results/reportho_lint.md)          |                                    -                                     |
 | :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 |      617 |     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 |      613 |     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)        |
@@ -106,7 +105,7 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
 | :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)       |
 | :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)        |
+| :white_check_mark: [scrnaseq](https://github.com/nf-core/scrnaseq)                             |     No      |      0 |       65 |     Yes     |         [View](lint_results/pipeline-results/scrnaseq_lint.md)          |        [View](lint_results/prints-help-results/scrnaseq_help.txt)        |
 | :x: [epigenomesegmentation](https://github.com/nf-core/epigenomesegmentation)                  |     No      |      0 |       59 |     No      |   [View](lint_results/pipeline-results/epigenomesegmentation_lint.md)   | [View](lint_results/prints-help-results/epigenomesegmentation_help.txt)  |
 | :x: [tumourevo](https://github.com/nf-core/tumourevo)                                          |     No      |      0 |       56 |     No      |         [View](lint_results/pipeline-results/tumourevo_lint.md)         |       [View](lint_results/prints-help-results/tumourevo_help.txt)        |
 | :white_check_mark: [mhcquant](https://github.com/nf-core/mhcquant)                             |     No      |      0 |       52 |     Yes     |         [View](lint_results/pipeline-results/mhcquant_lint.md)          |        [View](lint_results/prints-help-results/mhcquant_help.txt)        |
@@ -116,9 +115,10 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
 | :white_check_mark: [airrflow](https://github.com/nf-core/airrflow)                             |     No      |      0 |       40 |     Yes     |         [View](lint_results/pipeline-results/airrflow_lint.md)          |        [View](lint_results/prints-help-results/airrflow_help.txt)        |
 | :white_check_mark: [rnasplice](https://github.com/nf-core/rnasplice)                           |     No      |      0 |       34 |     Yes     |         [View](lint_results/pipeline-results/rnasplice_lint.md)         |       [View](lint_results/prints-help-results/rnasplice_help.txt)        |
 | :x: [stableexpression](https://github.com/nf-core/stableexpression)                            |     No      |      0 |       32 |     No      |     [View](lint_results/pipeline-results/stableexpression_lint.md)      |    [View](lint_results/prints-help-results/stableexpression_help.txt)    |
+| :white_check_mark: [scdownstream](https://github.com/nf-core/scdownstream)                     |     No      |      0 |       30 |     Yes     |       [View](lint_results/pipeline-results/scdownstream_lint.md)        |      [View](lint_results/prints-help-results/scdownstream_help.txt)      |
+| :white_check_mark: [rnafusion](https://github.com/nf-core/rnafusion)                           |     No      |      0 |       27 |     Yes     |         [View](lint_results/pipeline-results/rnafusion_lint.md)         |       [View](lint_results/prints-help-results/rnafusion_help.txt)        |
 | :white_check_mark: [funcprofiler](https://github.com/nf-core/funcprofiler)                     |     No      |      0 |       25 |     Yes     |       [View](lint_results/pipeline-results/funcprofiler_lint.md)        |      [View](lint_results/prints-help-results/funcprofiler_help.txt)      |
 | :white_check_mark: [mag](https://github.com/nf-core/mag)                                       |     No      |      0 |       25 |     Yes     |            [View](lint_results/pipeline-results/mag_lint.md)            |          [View](lint_results/prints-help-results/mag_help.txt)           |
-| :white_check_mark: [rnafusion](https://github.com/nf-core/rnafusion)                           |     No      |      0 |       24 |     Yes     |         [View](lint_results/pipeline-results/rnafusion_lint.md)         |       [View](lint_results/prints-help-results/rnafusion_help.txt)        |
 | :white_check_mark: [pairgenomealign](https://github.com/nf-core/pairgenomealign)               |     No      |      0 |       23 |     Yes     |      [View](lint_results/pipeline-results/pairgenomealign_lint.md)      |    [View](lint_results/prints-help-results/pairgenomealign_help.txt)     |
 | :x: [phaseimpute](https://github.com/nf-core/phaseimpute)                                      |     No      |      0 |       22 |     No      |        [View](lint_results/pipeline-results/phaseimpute_lint.md)        |      [View](lint_results/prints-help-results/phaseimpute_help.txt)       |
 | :white_check_mark: [variantbenchmarking](https://github.com/nf-core/variantbenchmarking)       |     No      |      0 |       22 |     Yes     |    [View](lint_results/pipeline-results/variantbenchmarking_lint.md)    |  [View](lint_results/prints-help-results/variantbenchmarking_help.txt)   |
@@ -127,7 +127,6 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
 | :x: [alleleexpression](https://github.com/nf-core/alleleexpression)                            |     No      |      0 |       20 |     No      |     [View](lint_results/pipeline-results/alleleexpression_lint.md)      |    [View](lint_results/prints-help-results/alleleexpression_help.txt)    |
 | :white_check_mark: [circrna](https://github.com/nf-core/circrna)                               |     No      |      0 |       20 |     Yes     |          [View](lint_results/pipeline-results/circrna_lint.md)          |        [View](lint_results/prints-help-results/circrna_help.txt)         |
 | :x: [dartseq](https://github.com/nf-core/dartseq)                                              |     No      |      0 |       19 |     No      |          [View](lint_results/pipeline-results/dartseq_lint.md)          |        [View](lint_results/prints-help-results/dartseq_help.txt)         |
-| :white_check_mark: [scdownstream](https://github.com/nf-core/scdownstream)                     |     No      |      0 |       19 |     Yes     |       [View](lint_results/pipeline-results/scdownstream_lint.md)        |      [View](lint_results/prints-help-results/scdownstream_help.txt)      |
 | :white_check_mark: [bacass](https://github.com/nf-core/bacass)                                 |     No      |      0 |       17 |     Yes     |          [View](lint_results/pipeline-results/bacass_lint.md)           |         [View](lint_results/prints-help-results/bacass_help.txt)         |
 | :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)       |
@@ -146,6 +145,7 @@ The goal is for all nf-core pipelines to run without errors using strict syntax.
 | :white_check_mark: [createtaxdb](https://github.com/nf-core/createtaxdb)                       |     No      |      0 |        6 |     Yes     |        [View](lint_results/pipeline-results/createtaxdb_lint.md)        |      [View](lint_results/prints-help-results/createtaxdb_help.txt)       |
 | :white_check_mark: [variantprioritization](https://github.com/nf-core/variantprioritization)   |     No      |      0 |        6 |     Yes     |   [View](lint_results/pipeline-results/variantprioritization_lint.md)   | [View](lint_results/prints-help-results/variantprioritization_help.txt)  |
 | :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: [scnanoseq](https://github.com/nf-core/scnanoseq)                           |     No      |      0 |        5 |     Yes     |         [View](lint_results/pipeline-results/scnanoseq_lint.md)         |       [View](lint_results/prints-help-results/scnanoseq_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)      |
 | :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)     |
@@ -189,8 +189,8 @@ _Modules with zero errors are not shown above (1853 modules). They may still hav
 
 ## Subworkflows
 
-- **Total:** 0 parse errors, 0 errors, 20 warnings across 116 subworkflows
-- **Zero errors:** 116 subworkflows (100.0%)
+- **Total:** 0 parse errors, 0 errors, 22 warnings across 117 subworkflows
+- **Zero errors:** 117 subworkflows (100.0%)
 
 |                     Errors                      |                      Warnings                       |
 | :---------------------------------------------: | :-------------------------------------------------: |
@@ -202,7 +202,7 @@ _Modules with zero errors are not shown above (1853 modules). They may still hav
 | Subworkflow | Parse Error | Errors | Warnings | Lint Output |
 | ----------- | :---------: | -----: | -------: | :---------: |
 
-_Subworkflows with zero errors are not shown above (116 subworkflows). They may still have warnings. See the [subworkflows results directory](lint_results/subworkflow-results/) for all lint outputs._
+_Subworkflows with zero errors are not shown above (117 subworkflows). They may still have warnings. See the [subworkflows results directory](lint_results/subworkflow-results/) for all lint outputs._
 
 </details>
 

lint_results/module-results/abacas_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-28T00:41:17.298835+00:00
-- Nextflow version: 26.04.2
+- Generated: 2026-05-29T00:45:36.919896+00:00
+- Nextflow version: 26.04.3
 - Summary: No issues found

lint_results/module-results/abra2_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-28T00:41:17.299034+00:00
-- Nextflow version: 26.04.2
+- Generated: 2026-05-29T00:45:36.920078+00:00
+- Nextflow version: 26.04.3
 - Summary: No issues found

lint_results/module-results/abricate_run_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-28T00:41:17.299179+00:00
-- Nextflow version: 26.04.2
+- Generated: 2026-05-29T00:45:36.920215+00:00
+- Nextflow version: 26.04.3
 - Summary: No issues found

lint_results/module-results/abricate_summary_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-28T00:41:17.299344+00:00
-- Nextflow version: 26.04.2
+- Generated: 2026-05-29T00:45:36.920313+00:00
+- Nextflow version: 26.04.3
 - Summary: No issues found

lint_results/module-results/abritamr_run_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-28T00:41:17.299485+00:00
-- Nextflow version: 26.04.2
+- Generated: 2026-05-29T00:45:36.920402+00:00
+- Nextflow version: 26.04.3
 - Summary: No issues found

lint_results/module-results/abyss_abysspe_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-28T00:41:17.299618+00:00
-- Nextflow version: 26.04.2
+- Generated: 2026-05-29T00:45:36.920487+00:00
+- Nextflow version: 26.04.3
 - Summary: No issues found

lint_results/module-results/adapterremoval_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-28T00:41:17.299749+00:00
-- Nextflow version: 26.04.2
+- Generated: 2026-05-29T00:45:36.920571+00:00
+- Nextflow version: 26.04.3
 - Summary: No issues found

lint_results/module-results/adapterremovalfixprefix_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-28T00:41:17.299878+00:00
-- Nextflow version: 26.04.2
+- Generated: 2026-05-29T00:45:36.920652+00:00
+- Nextflow version: 26.04.3
 - Summary: No issues found

lint_results/module-results/admixture_lint.md

@@ -1,5 +1,5 @@
 # Nextflow lint results
 
-- Generated: 2026-05-28T00:41:17.300006+00:00
-- Nextflow version: 26.04.2
+- Generated: 2026-05-29T00:45:36.920734+00:00
+- Nextflow version: 26.04.3
 - Summary: No issues found