From 03b60d3f4430b381bee9d83805010b8ac38b9da4 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Fri, 17 Apr 2026 20:16:07 +0000
Subject: [PATCH 01/29] migrate
 `ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION` to seqera containers

---
 .../gtf2featureannotation/main.nf                             | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf
index 6b0e3e82121b..c3a1b0dc90c1 100644
--- a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf
+++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf
@@ -4,8 +4,8 @@ process ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/atlas-gene-annotation-manipulation%3A1.1.1--hdfd78af_0':
-        'biocontainers/atlas-gene-annotation-manipulation:1.1.1--hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a0/a0dc845564dcc40319d4b76a9f7298fd83ccd9eb271153c688f41660cda7de0f/data':
+        'community.wave.seqera.io/library/atlas-gene-annotation-manipulation:1.1.1--b9e8c32c92709512' }"
 
     input:
     tuple val(meta), path(gtf)

From f3d486422d7519ac4b710e16c88d7f72d21fa714 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Fri, 17 Apr 2026 20:16:58 +0000
Subject: [PATCH 02/29] migrate `AFFY_JUSTRMA` to seqera containers

---
 modules/nf-core/affy/justrma/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/affy/justrma/main.nf b/modules/nf-core/affy/justrma/main.nf
index 4de23d18b24c..c09d9b4aa9aa 100644
--- a/modules/nf-core/affy/justrma/main.nf
+++ b/modules/nf-core/affy/justrma/main.nf
@@ -4,8 +4,8 @@ process AFFY_JUSTRMA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-affy:1.78.0--r43ha9d7317_1':
-        'biocontainers/bioconductor-affy:1.78.0--r43ha9d7317_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/62/62d22bc460807a1a4ded40e5b7a391aa6f2dac189d4153d684472d65333ca8d4/data':
+        'community.wave.seqera.io/library/bioconductor-affy_r-base:dd8a5ecd6fc301b3' }"
 
     input:
     tuple val(meta), path(samplesheet), path(celfiles_dir)

From 975739de5a9392c06b201ea420c273d3b6d0ddc3 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 20 Apr 2026 13:07:51 +0000
Subject: [PATCH 03/29] add `csvtk_join` seqera containers

---
 modules/nf-core/csvtk/join/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/csvtk/join/main.nf b/modules/nf-core/csvtk/join/main.nf
index 46c9f3009db8..f9f678427e4b 100644
--- a/modules/nf-core/csvtk/join/main.nf
+++ b/modules/nf-core/csvtk/join/main.nf
@@ -4,8 +4,8 @@ process CSVTK_JOIN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/csvtk:0.31.0--h9ee0642_0':
-        'biocontainers/csvtk:0.31.0--h9ee0642_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c818804e2e954ab8bc52c8bdc961539d2aa0a6b0f9517c3a6118d5a6c6a38669/data':
+        'community.wave.seqera.io/library/csvtk:0.31.0--483af3c969467fe4' }"
 
     input:
     tuple val(meta), path(csv)

From 6fdfbf0d28a7baf27db0ea7c1f3f257e160f257f Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 20 Apr 2026 13:22:34 +0000
Subject: [PATCH 04/29] add containers to CUSTOM_FILTERDIFFERENTIALTABLE

---
 modules/nf-core/custom/filterdifferentialtable/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/custom/filterdifferentialtable/main.nf b/modules/nf-core/custom/filterdifferentialtable/main.nf
index 98461f249d5c..cad5d3839fda 100644
--- a/modules/nf-core/custom/filterdifferentialtable/main.nf
+++ b/modules/nf-core/custom/filterdifferentialtable/main.nf
@@ -4,8 +4,8 @@ process CUSTOM_FILTERDIFFERENTIALTABLE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pandas:1.5.2' :
-        'biocontainers/pandas:1.5.2' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4d/4d7a62daafff045d7ea7739aac6e24d495ab94512525d73bcd865f5cf27cfe0f/data' :
+        'community.wave.seqera.io/library/pandas:1.5.2--8aad09419bb2ac73' }"
 
     input:
     tuple val(meta), path(input_file)

From 4a56e4a4044588e51ff4b5d9177ff48b76b4d81e Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 20 Apr 2026 13:25:37 +0000
Subject: [PATCH 05/29] add seqera containers to CUSTOM_TABULARTOGSEACHIP

---
 modules/nf-core/custom/tabulartogseachip/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/custom/tabulartogseachip/main.nf b/modules/nf-core/custom/tabulartogseachip/main.nf
index c0622cda518d..86fe994600ef 100644
--- a/modules/nf-core/custom/tabulartogseachip/main.nf
+++ b/modules/nf-core/custom/tabulartogseachip/main.nf
@@ -4,8 +4,8 @@ process CUSTOM_TABULARTOGSEACHIP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
-        'biocontainers/gawk:5.1.0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ca/cae75dbf13aabe63298c0acce8ccfa9bd65fe4b73dc5578da5a2e30867f7169f/data' :
+        'community.wave.seqera.io/library/gawk:5.1.0--fa97c4ccf4cfbc4b' }"
 
     input:
     tuple val(meta), path(tabular)

From 3abba1240c56d10838a76d828fca1cfb914c8e47 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 20 Apr 2026 13:35:40 +0000
Subject: [PATCH 06/29] add seqera containers to GEOQUERY_GETGEO

---
 modules/nf-core/geoquery/getgeo/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/geoquery/getgeo/main.nf b/modules/nf-core/geoquery/getgeo/main.nf
index ec32b43d5cf2..b985e7e018ed 100644
--- a/modules/nf-core/geoquery/getgeo/main.nf
+++ b/modules/nf-core/geoquery/getgeo/main.nf
@@ -4,8 +4,8 @@ process GEOQUERY_GETGEO {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-geoquery:2.70.0--r43hdfd78af_0' :
-        'biocontainers/bioconductor-geoquery:2.70.0--r43hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c3/c367777a9f3947bdfc464c3cec52d33d2862c5e909fa77e13455f8c1d177767b/data' :
+        'community.wave.seqera.io/library/bioconductor-geoquery_r-base:8547a00389cd568a' }"
 
     input:
     tuple val(meta), val(querygse)

From d00855890f666b5023681fdddc749fa6ce5f0f3c Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 20 Apr 2026 13:51:42 +0000
Subject: [PATCH 07/29] update to seqera containers proteus

---
 modules/nf-core/proteus/readproteingroups/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/proteus/readproteingroups/main.nf b/modules/nf-core/proteus/readproteingroups/main.nf
index c9ab04e59ea6..3d65ec89c760 100644
--- a/modules/nf-core/proteus/readproteingroups/main.nf
+++ b/modules/nf-core/proteus/readproteingroups/main.nf
@@ -4,8 +4,8 @@ process PROTEUS_READPROTEINGROUPS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-503e259d7d34ce533ce66c4c8871af4ab409db6d:1e504ef71c83943061a39b6260d826b988bfa56f-0':
-        'biocontainers/mulled-v2-503e259d7d34ce533ce66c4c8871af4ab409db6d:1e504ef71c83943061a39b6260d826b988bfa56f-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d0/d0008e2c0054e7cb33f3acef6ea417d157945a6f5774f6b7bdc1ef19cf95b249/data':
+        'community.wave.seqera.io/library/bioconductor-limma_r-proteus-bartongroup_r-base_r-ggplot2_r-plotly:855c86e2407bbedb' }"
 
     input:
     tuple val(meta), path(samplesheet), path(intensities)

From bccf768ee4e3e9c6203bffa64263ebc1074542f1 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 20 Apr 2026 13:53:52 +0000
Subject: [PATCH 08/29] migrate to seqera containers zip

---
 modules/nf-core/zip/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/zip/main.nf b/modules/nf-core/zip/main.nf
index d0fe8666f6bd..b830162623eb 100644
--- a/modules/nf-core/zip/main.nf
+++ b/modules/nf-core/zip/main.nf
@@ -4,8 +4,8 @@ process ZIP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/p7zip:16.02' :
-        'biocontainers/p7zip:16.02' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/17/171e3d1c631246d5afa0f01e78e0ff6a6ee78012dd17a7e8eccc871b65eac258/data' :
+        'community.wave.seqera.io/library/p7zip:16.02--94efedc6cfea7db9' }"
 
     input:
     tuple val(meta), path(files, stageAs: "inputs/*")

From 17d1b573f20256406c80afb101acff7c15639bbf Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 20 Apr 2026 15:06:16 +0000
Subject: [PATCH 09/29] migrate to topics template scripts

---
 modules/nf-core/geoquery/getgeo/main.nf           | 2 +-
 modules/nf-core/proteus/readproteingroups/main.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/geoquery/getgeo/main.nf b/modules/nf-core/geoquery/getgeo/main.nf
index b985e7e018ed..04ba5a1dc46e 100644
--- a/modules/nf-core/geoquery/getgeo/main.nf
+++ b/modules/nf-core/geoquery/getgeo/main.nf
@@ -14,7 +14,7 @@ process GEOQUERY_GETGEO {
     tuple val(meta), path("*.rds")            , emit: rds
     tuple val(meta), path("*matrix.tsv")      , emit: expression
     tuple val(meta), path("*annotation.tsv")  , emit: annotation
-    path "versions.yml"                       , emit: versions
+    path "versions.yml"                       , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/proteus/readproteingroups/main.nf b/modules/nf-core/proteus/readproteingroups/main.nf
index 3d65ec89c760..241ef3c06bd3 100644
--- a/modules/nf-core/proteus/readproteingroups/main.nf
+++ b/modules/nf-core/proteus/readproteingroups/main.nf
@@ -20,7 +20,7 @@ process PROTEUS_READPROTEINGROUPS {
     tuple val(meta), path("*raw_proteingroups_tab.tsv")         , emit: raw_tab
     tuple val(meta), path("*normalized_proteingroups_tab.tsv")  , emit: norm_tab
     tuple val(meta), path("*R_sessionInfo.log")                 , emit: session_info
-    path "versions.yml"                                         , emit: versions
+    path "versions.yml"                                         , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

From 67492186646c3c60c8fcaf47590d4f88bdd87d8e Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 20 Apr 2026 15:14:12 +0000
Subject: [PATCH 10/29] add versions to tabulartogseachip

---
 modules/nf-core/custom/tabulartogseachip/main.nf | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/custom/tabulartogseachip/main.nf b/modules/nf-core/custom/tabulartogseachip/main.nf
index 86fe994600ef..7622c5eb6347 100644
--- a/modules/nf-core/custom/tabulartogseachip/main.nf
+++ b/modules/nf-core/custom/tabulartogseachip/main.nf
@@ -13,7 +13,7 @@ process CUSTOM_TABULARTOGSEACHIP {
 
     output:
     tuple val(meta), path("*.chip"), emit: chip
-    path "versions.yml"            , emit: versions
+    tuple val("${task.process}"), val('CUSTOM_TABULARTOGSEACHIP'), eval("awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//'"), emit: versions_custom_tabulartogseachip, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -36,10 +36,6 @@ process CUSTOM_TABULARTOGSEACHIP {
     tail -n +2 $tabular | awk -F'\\t' -v id=\$id_col -v symbol=\$symbol_col '{print \$id"\\t"\$symbol"\\tNA"}' >> \${outfile}.tmp
     mv \${outfile}.tmp \${outfile}
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -48,9 +44,6 @@ process CUSTOM_TABULARTOGSEACHIP {
     outfile=${prefix}.chip
     touch \$outfile
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
-    END_VERSIONS
+
     """
 }

From 222062334fb79ee344327e36c470ee3117b77e42 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 20 Apr 2026 15:22:44 +0000
Subject: [PATCH 11/29] add versions to zip

---
 modules/nf-core/zip/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/zip/main.nf b/modules/nf-core/zip/main.nf
index b830162623eb..b67327335408 100644
--- a/modules/nf-core/zip/main.nf
+++ b/modules/nf-core/zip/main.nf
@@ -12,7 +12,7 @@ process ZIP {
 
     output:
     tuple val(meta), path("${prefix}.zip"), emit: zipped_archive
-    path "versions.yml"                   , emit: versions
+    tuple val("${task.process}"), val('zip'), eval("7za --help | sed 's/.*p7zip Version //; s/(.*//'"), emit: versions_zip, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

From 920bfd2d35cac8f7f7e62d5985b92505220a3104 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 20 Apr 2026 15:28:15 +0000
Subject: [PATCH 12/29] update meta.yml zip

---
 modules/nf-core/zip/meta.yml | 35 +++++++++++++++++++++++++----------
 1 file changed, 25 insertions(+), 10 deletions(-)

diff --git a/modules/nf-core/zip/meta.yml b/modules/nf-core/zip/meta.yml
index 81624fc817e7..4e8710219944 100644
--- a/modules/nf-core/zip/meta.yml
+++ b/modules/nf-core/zip/meta.yml
@@ -7,12 +7,13 @@ keywords:
   - archiving
 tools:
   - unzip:
-      description: p7zip is a quick port of 7z.exe and 7za.exe (command line version
-        of 7zip, see www.7-zip.org) for Unix.
+      description: p7zip is a quick port of 7z.exe and 7za.exe (command line
+        version of 7zip, see www.7-zip.org) for Unix.
       homepage: https://sourceforge.net/projects/p7zip/
       documentation: https://sourceforge.net/projects/p7zip/
       tool_dev_url: https://sourceforge.net/projects/p7zip"
-      licence: ["LGPL-2.1-or-later"]
+      licence:
+        - "LGPL-2.1-or-later"
       identifier: ""
 input:
   - - meta:
@@ -36,14 +37,28 @@ output:
           description: ZIP file
           pattern: "*.zip"
           ontologies:
-            - edam: http://edamontology.org/format_3987 # ZIP format
+            - edam: http://edamontology.org/format_3987
+  versions_zip:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - zip:
+          type: string
+          description: The name of the tool
+      - 7za --help | sed 's/.*p7zip Version //; s/(.*//':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - zip:
+          type: string
+          description: The name of the tool
+      - 7za --help | sed 's/.*p7zip Version //; s/(.*//':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@jfy133"
   - "@pinin4fjords"

From 7a3c996bcfa73179ffd02a1c2781fde5d39906c4 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 20 Apr 2026 15:43:53 +0000
Subject: [PATCH 13/29] update meta.yml

---
 .../custom/filterdifferentialtable/meta.yml   | 25 +++++++++--------
 .../nf-core/custom/tabulartogseachip/meta.yml | 28 ++++++++++++++-----
 modules/nf-core/geoquery/getgeo/meta.yml      | 14 +++++++---
 .../proteus/readproteingroups/meta.yml        | 10 +++++--
 4 files changed, 53 insertions(+), 24 deletions(-)

diff --git a/modules/nf-core/custom/filterdifferentialtable/meta.yml b/modules/nf-core/custom/filterdifferentialtable/meta.yml
index 9ee9c6b393f0..b87159857f69 100644
--- a/modules/nf-core/custom/filterdifferentialtable/meta.yml
+++ b/modules/nf-core/custom/filterdifferentialtable/meta.yml
@@ -1,6 +1,6 @@
 name: "custom_filterdifferentialtable"
-description: Filters a differential expression table based on logFC and adjusted p-value
-  thresholds
+description: Filters a differential expression table based on logFC and adjusted
+  p-value thresholds
 keywords:
   - filter
   - differential expression
@@ -14,7 +14,8 @@ tools:
       documentation: "https://pandas.pydata.org/docs/"
       tool_dev_url: "https://github.com/pandas-dev/pandas"
       doi: "10.5281/zenodo.3509134"
-      licence: ["BSD-3-Clause"]
+      licence:
+        - "BSD-3-Clause"
       identifiers:
         - "biotools:pandas"
         - "conda:pandas"
@@ -30,8 +31,8 @@ input:
         description: Input differential expression table (CSV, TSV, or TXT format)
         pattern: "*.{csv,tsv,txt}"
         ontologies:
-          - edam: http://edamontology.org/format_3752 # CSV
-          - edam: http://edamontology.org/format_3475 # TSV
+          - edam: http://edamontology.org/format_3752
+          - edam: http://edamontology.org/format_3475
   - - logfc_column:
         type: string
         description: Name of the column containing log fold change values
@@ -68,7 +69,7 @@ output:
           description: Filtered differential expression table
           pattern: "*_filtered.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   filtered_up:
     - - meta:
           type: map
@@ -77,10 +78,11 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*_filtered_up.tsv":
           type: file
-          description: Filtered differential expression table for overexpressed genes
+          description: Filtered differential expression table for overexpressed
+            genes
           pattern: "*_filtered_up.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   filtered_down:
     - - meta:
           type: map
@@ -89,17 +91,18 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*_filtered_down.tsv":
           type: file
-          description: Filtered differential expression table for underexpressed genes
+          description: Filtered differential expression table for underexpressed
+            genes
           pattern: "*_filtered_down.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   versions:
     - versions.yml:
         type: file
         description: File containing software versions
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3750
 authors:
   - "@pinin4fjords"
   - "@WackerO"
diff --git a/modules/nf-core/custom/tabulartogseachip/meta.yml b/modules/nf-core/custom/tabulartogseachip/meta.yml
index 7dddadc3612d..8fe550555272 100644
--- a/modules/nf-core/custom/tabulartogseachip/meta.yml
+++ b/modules/nf-core/custom/tabulartogseachip/meta.yml
@@ -24,7 +24,7 @@ input:
           features ids, and another column with the features symbols.
         pattern: "*.{tsv}"
         ontologies:
-          - edam: http://edamontology.org/format_3475 # TSV
+          - edam: http://edamontology.org/format_3475
   - - id:
         type: string
         description: The name of the column containing feature ids
@@ -44,13 +44,27 @@ output:
             https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats
           pattern: "*.chip"
           ontologies: []
+  versions_custom_tabulartogseachip:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - CUSTOM_TABULARTOGSEACHIP:
+          type: string
+          description: The name of the tool
+      - awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - CUSTOM_TABULARTOGSEACHIP:
+          type: string
+          description: The name of the tool
+      - awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@pinin4fjords"
   - "@suzannejin"
diff --git a/modules/nf-core/geoquery/getgeo/meta.yml b/modules/nf-core/geoquery/getgeo/meta.yml
index 04ca904f6cb8..7631c0887acf 100644
--- a/modules/nf-core/geoquery/getgeo/meta.yml
+++ b/modules/nf-core/geoquery/getgeo/meta.yml
@@ -11,7 +11,8 @@ tools:
       documentation: "https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html"
       tool_dev_url: "https://github.com/seandavi/GEOquery"
       doi: "10.1093/bioinformatics/btm254"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: biotools:geoquery
 input:
   - - meta:
@@ -41,7 +42,7 @@ output:
           description: TSV-format expression matrix
           pattern: "*matrix.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   annotation:
     - - meta:
           type: map
@@ -51,14 +52,19 @@ output:
           description: TSV-format annotation file
           pattern: "*annotation.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   versions:
     - versions.yml:
         type: file
         description: File containing software versions
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3750
+topics:
+  versions:
+    - versions.yml:
+        type: string
+        description: The name of the process
 authors:
   - "@azedinez"
   - "@pinin4fjords"
diff --git a/modules/nf-core/proteus/readproteingroups/meta.yml b/modules/nf-core/proteus/readproteingroups/meta.yml
index 5f5e8f57faff..29f41882a2e5 100644
--- a/modules/nf-core/proteus/readproteingroups/meta.yml
+++ b/modules/nf-core/proteus/readproteingroups/meta.yml
@@ -11,7 +11,8 @@ tools:
       documentation: "https://rdrr.io/github/bartongroup/Proteus/"
       tool_dev_url: "https://github.com/bartongroup/Proteus"
       doi: "10.1101/416511"
-      licence: ["GPL v2"]
+      licence:
+        - "GPL v2"
       identifier: biotools:proteus-engineering
 input:
   - - meta:
@@ -134,7 +135,12 @@ output:
         description: File containing software versions
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3750
+topics:
+  versions:
+    - versions.yml:
+        type: string
+        description: The name of the process
 authors:
   - "@WackerO"
 maintainers:

From e0f638cf313a7ead8056b27729826a86d96dd35d Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 20 Apr 2026 15:51:58 +0000
Subject: [PATCH 14/29] update meta.yml

---
 .../custom/filterdifferentialtable/main.nf    |  7 +----
 .../custom/filterdifferentialtable/meta.yml   | 26 ++++++++++++++-----
 2 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/modules/nf-core/custom/filterdifferentialtable/main.nf b/modules/nf-core/custom/filterdifferentialtable/main.nf
index cad5d3839fda..12f5e936f0d7 100644
--- a/modules/nf-core/custom/filterdifferentialtable/main.nf
+++ b/modules/nf-core/custom/filterdifferentialtable/main.nf
@@ -16,7 +16,7 @@ process CUSTOM_FILTERDIFFERENTIALTABLE {
     tuple val(meta), path("*_filtered.tsv")         , emit: filtered
     tuple val(meta), path("*_filtered_up.tsv")      , emit: filtered_up
     tuple val(meta), path("*_filtered_down.tsv")    , emit: filtered_down
-    path "versions.yml"                             , emit: versions
+    tuple val("${task.process}"), val('CUSTOM_FILTERDIFFERENTIALTABLE'), eval("python -c \"import pandas as pd; print(pd.__version__)\""), emit: versions_customfilterdifferentialtable, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -71,10 +71,6 @@ process CUSTOM_FILTERDIFFERENTIALTABLE {
     filtered_table_up.to_csv("${prefix}_filtered_up.tsv", sep='\t', index=False)
     filtered_table_down.to_csv("${prefix}_filtered_down.tsv", sep='\t', index=False)
 
-    # Write versions
-    with open('versions.yml', 'w') as version_file:
-        version_file.write('"${task.process}":\\n')
-        version_file.write(f"    pandas: {pd.__version__}\\n")
     """
 
     stub:
@@ -83,6 +79,5 @@ process CUSTOM_FILTERDIFFERENTIALTABLE {
     touch ${prefix}_filtered.tsv
     touch ${prefix}_filtered_up.tsv
     touch ${prefix}_filtered_down.tsv
-    echo '"${task.process}":\\n    pandas: 1.5.2' > versions.yml
     """
 }
diff --git a/modules/nf-core/custom/filterdifferentialtable/meta.yml b/modules/nf-core/custom/filterdifferentialtable/meta.yml
index b87159857f69..4a7d37588969 100644
--- a/modules/nf-core/custom/filterdifferentialtable/meta.yml
+++ b/modules/nf-core/custom/filterdifferentialtable/meta.yml
@@ -96,13 +96,27 @@ output:
           pattern: "*_filtered_down.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475
+  versions_customfilterdifferentialtable:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - CUSTOM_FILTERDIFFERENTIALTABLE:
+          type: string
+          description: The name of the tool
+      - python -c "import pandas as pd; print(pd.__version__)":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - CUSTOM_FILTERDIFFERENTIALTABLE:
+          type: string
+          description: The name of the tool
+      - python -c "import pandas as pd; print(pd.__version__)":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@pinin4fjords"
   - "@WackerO"

From 8604b70c64b9a69627934ff929e86d601134f0d1 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 21 Apr 2026 16:53:40 +0000
Subject: [PATCH 15/29] update zip snap

---
 modules/nf-core/zip/tests/main.nf.test.snap | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/zip/tests/main.nf.test.snap b/modules/nf-core/zip/tests/main.nf.test.snap
index ee29e2813e74..ba8cb85ac1f6 100644
--- a/modules/nf-core/zip/tests/main.nf.test.snap
+++ b/modules/nf-core/zip/tests/main.nf.test.snap
@@ -1,10 +1,10 @@
 {
     "versions": {
-        "content": [
-            [
-                "versions.yml:md5,721b9a1e22ba1d75fe6a30bb1684cf02"
-            ]
-        ],
-        "timestamp": "2023-11-28T18:31:32.386325319"
+        "content": null,
+        "timestamp": "2026-04-20T19:15:55.112565364",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file

From cd3a714a742bf2705e5113da0e41b918881c01e6 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 21 Apr 2026 16:56:27 +0000
Subject: [PATCH 16/29] remove version collection from
 CUSTOM_FILTERDIFFERENTIALTABLE

---
 subworkflows/nf-core/abundance_differential_filter/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/subworkflows/nf-core/abundance_differential_filter/main.nf b/subworkflows/nf-core/abundance_differential_filter/main.nf
index 81836f03b528..9a66992dc4f7 100644
--- a/subworkflows/nf-core/abundance_differential_filter/main.nf
+++ b/subworkflows/nf-core/abundance_differential_filter/main.nf
@@ -255,7 +255,6 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER {
         ch_diff_filter_params.fc_input,
         ch_diff_filter_params.stat_input
     )
-    ch_versions = ch_versions.mix(CUSTOM_FILTERDIFFERENTIALTABLE.out.versions.first())
 
     emit:
 

From f2e38ad74d89d75a62e3add15751ae1aded758a2 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 21 Apr 2026 17:05:19 +0000
Subject: [PATCH 17/29] remove version collection from CUSTOM_TABULARTOGSEACHIP

---
 subworkflows/nf-core/differential_functional_enrichment/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/subworkflows/nf-core/differential_functional_enrichment/main.nf b/subworkflows/nf-core/differential_functional_enrichment/main.nf
index 2ae98aac8314..a7fdaeccbfd6 100644
--- a/subworkflows/nf-core/differential_functional_enrichment/main.nf
+++ b/subworkflows/nf-core/differential_functional_enrichment/main.nf
@@ -153,7 +153,6 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT {
         .mix(GPROFILER2_GOST.out.versions)
         .mix(CUSTOM_TABULARTOGSEAGCT.out.versions)
         .mix(CUSTOM_TABULARTOGSEACLS.out.versions)
-        .mix(CUSTOM_TABULARTOGSEACHIP.out.versions)
         .mix(DECOUPLER_DECOUPLER.out.versions)
         .mix(PROPR_GREA.out.versions)
 

From f5fcc3cb5e416d15bf2ce664967bf289a57c759d Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 21 Apr 2026 17:13:16 +0000
Subject: [PATCH 18/29] Process output of type 'eval' is only allowed with Bash
 process scripts

---
 modules/nf-core/custom/filterdifferentialtable/main.nf | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/custom/filterdifferentialtable/main.nf b/modules/nf-core/custom/filterdifferentialtable/main.nf
index 12f5e936f0d7..73dbbd219492 100644
--- a/modules/nf-core/custom/filterdifferentialtable/main.nf
+++ b/modules/nf-core/custom/filterdifferentialtable/main.nf
@@ -16,7 +16,7 @@ process CUSTOM_FILTERDIFFERENTIALTABLE {
     tuple val(meta), path("*_filtered.tsv")         , emit: filtered
     tuple val(meta), path("*_filtered_up.tsv")      , emit: filtered_up
     tuple val(meta), path("*_filtered_down.tsv")    , emit: filtered_down
-    tuple val("${task.process}"), val('CUSTOM_FILTERDIFFERENTIALTABLE'), eval("python -c \"import pandas as pd; print(pd.__version__)\""), emit: versions_customfilterdifferentialtable, topic: versions
+    path "versions.yml", emit: versions_customfilterdifferentialtable, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -71,6 +71,11 @@ process CUSTOM_FILTERDIFFERENTIALTABLE {
     filtered_table_up.to_csv("${prefix}_filtered_up.tsv", sep='\t', index=False)
     filtered_table_down.to_csv("${prefix}_filtered_down.tsv", sep='\t', index=False)
 
+    # Write versions
+    with open('versions.yml', 'w') as version_file:
+        version_file.write('"${task.process}":\\n')
+        version_file.write(f"    pandas: {pd.__version__}\\n")
+
     """
 
     stub:
@@ -79,5 +84,6 @@ process CUSTOM_FILTERDIFFERENTIALTABLE {
     touch ${prefix}_filtered.tsv
     touch ${prefix}_filtered_up.tsv
     touch ${prefix}_filtered_down.tsv
+    echo '"${task.process}":\\n    pandas: 1.5.2' > versions.yml
     """
 }

From b52972c3c3ce624d5f00d777afa7fecca9d202ab Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 21 Apr 2026 17:20:20 +0000
Subject: [PATCH 19/29] modify meta.yml

---
 .../custom/filterdifferentialtable/meta.yml   | 27 +++++++------------
 1 file changed, 9 insertions(+), 18 deletions(-)

diff --git a/modules/nf-core/custom/filterdifferentialtable/meta.yml b/modules/nf-core/custom/filterdifferentialtable/meta.yml
index 4a7d37588969..e3f024548570 100644
--- a/modules/nf-core/custom/filterdifferentialtable/meta.yml
+++ b/modules/nf-core/custom/filterdifferentialtable/meta.yml
@@ -97,26 +97,17 @@ output:
           ontologies:
             - edam: http://edamontology.org/format_3475
   versions_customfilterdifferentialtable:
-    - - ${task.process}:
-          type: string
-          description: The name of the process
-      - CUSTOM_FILTERDIFFERENTIALTABLE:
-          type: string
-          description: The name of the tool
-      - python -c "import pandas as pd; print(pd.__version__)":
-          type: eval
-          description: The expression to obtain the version of the tool
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
 topics:
   versions:
-    - - ${task.process}:
-          type: string
-          description: The name of the process
-      - CUSTOM_FILTERDIFFERENTIALTABLE:
-          type: string
-          description: The name of the tool
-      - python -c "import pandas as pd; print(pd.__version__)":
-          type: eval
-          description: The expression to obtain the version of the tool
+    - versions.yml:
+        type: string
+        description: The name of the process
 authors:
   - "@pinin4fjords"
   - "@WackerO"

From 1d2d13d6692a6eda1b77173afd4fff0c6eeddae4 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 21 Apr 2026 17:34:29 +0000
Subject: [PATCH 20/29] update versions zip

---
 modules/nf-core/zip/main.nf                 |  7 +------
 modules/nf-core/zip/tests/main.nf.test      |  4 +++-
 modules/nf-core/zip/tests/main.nf.test.snap | 14 ++++++++++++--
 3 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/zip/main.nf b/modules/nf-core/zip/main.nf
index b67327335408..2f15d6954f60 100644
--- a/modules/nf-core/zip/main.nf
+++ b/modules/nf-core/zip/main.nf
@@ -12,7 +12,7 @@ process ZIP {
 
     output:
     tuple val(meta), path("${prefix}.zip"), emit: zipped_archive
-    tuple val("${task.process}"), val('zip'), eval("7za --help | sed 's/.*p7zip Version //; s/(.*//'"), emit: versions_zip, topic: versions
+    tuple val("${task.process}"), val('zip'), eval("7za i 2>&1 | grep 'p7zip Version' | sed 's/.*p7zip Version //; s/(.*//'"), emit: versions_zip, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,10 +27,5 @@ process ZIP {
         -l \\
         $args \\
         "${prefix}.zip" ./inputs/*
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/zip/tests/main.nf.test b/modules/nf-core/zip/tests/main.nf.test
index 9652841d3601..2367a1284f31 100644
--- a/modules/nf-core/zip/tests/main.nf.test
+++ b/modules/nf-core/zip/tests/main.nf.test
@@ -24,7 +24,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert path(process.out.zipped_archive.get(0).get(1)).exists() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(
+                    process.out.findAll { key, val -> key.startsWith('versions') },
+                    ).match("versions") }
             )
         }
     }
diff --git a/modules/nf-core/zip/tests/main.nf.test.snap b/modules/nf-core/zip/tests/main.nf.test.snap
index ba8cb85ac1f6..e02ab8a29f6b 100644
--- a/modules/nf-core/zip/tests/main.nf.test.snap
+++ b/modules/nf-core/zip/tests/main.nf.test.snap
@@ -1,7 +1,17 @@
 {
     "versions": {
-        "content": null,
-        "timestamp": "2026-04-20T19:15:55.112565364",
+        "content": [
+            {
+                "versions_zip": [
+                    [
+                        "ZIP",
+                        "zip",
+                        "16.02 "
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-21T17:33:25.048503257",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

From f95622997bfc729d88918280762ca812cbeea197 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 21 Apr 2026 18:03:37 +0000
Subject: [PATCH 21/29] remove publishDir

---
 modules/nf-core/limma/differential/tests/nextflow.config        | 2 --
 .../limma/differential/tests/nextflow.exclude_samples.config    | 2 --
 .../limma/differential/tests/nextflow.interaction.config        | 2 --
 .../limma/differential/tests/nextflow.subset_to_contrast.config | 2 --
 modules/nf-core/limma/differential/tests/nextflow.voom.config   | 2 --
 .../limma/differential/tests/nextflow.voom_blocking.config      | 2 --
 .../nf-core/limma/differential/tests/nextflow.voom_mixed.config | 2 --
 .../limma/differential/tests/nextflow.voom_mixed_seed.config    | 2 --
 8 files changed, 16 deletions(-)

diff --git a/modules/nf-core/limma/differential/tests/nextflow.config b/modules/nf-core/limma/differential/tests/nextflow.config
index 98c5e882164e..2e799d2562b4 100644
--- a/modules/nf-core/limma/differential/tests/nextflow.config
+++ b/modules/nf-core/limma/differential/tests/nextflow.config
@@ -1,7 +1,5 @@
 process {
 
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: 'LIMMA_DIFFERENTIAL' {
         ext.args = { [
             "--sample_id_col name",
diff --git a/modules/nf-core/limma/differential/tests/nextflow.exclude_samples.config b/modules/nf-core/limma/differential/tests/nextflow.exclude_samples.config
index 1f4c02141582..015556080742 100644
--- a/modules/nf-core/limma/differential/tests/nextflow.exclude_samples.config
+++ b/modules/nf-core/limma/differential/tests/nextflow.exclude_samples.config
@@ -1,7 +1,5 @@
 process {
 
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: 'LIMMA_DIFFERENTIAL' {
         ext.args = { [
             "--sample_id_col name",
diff --git a/modules/nf-core/limma/differential/tests/nextflow.interaction.config b/modules/nf-core/limma/differential/tests/nextflow.interaction.config
index f73bf1d62f8a..aafda5f3fb16 100644
--- a/modules/nf-core/limma/differential/tests/nextflow.interaction.config
+++ b/modules/nf-core/limma/differential/tests/nextflow.interaction.config
@@ -1,7 +1,5 @@
 process {
 
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: 'LIMMA_DIFFERENTIAL' {
         ext.args = { [
             "--sample_id_col sample",
diff --git a/modules/nf-core/limma/differential/tests/nextflow.subset_to_contrast.config b/modules/nf-core/limma/differential/tests/nextflow.subset_to_contrast.config
index 09d6776b203e..57aaf7e8338d 100644
--- a/modules/nf-core/limma/differential/tests/nextflow.subset_to_contrast.config
+++ b/modules/nf-core/limma/differential/tests/nextflow.subset_to_contrast.config
@@ -1,7 +1,5 @@
 process {
 
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: 'LIMMA_DIFFERENTIAL' {
         ext.args = { [
             "--sample_id_col name",
diff --git a/modules/nf-core/limma/differential/tests/nextflow.voom.config b/modules/nf-core/limma/differential/tests/nextflow.voom.config
index a1e505570e13..defe285a5164 100644
--- a/modules/nf-core/limma/differential/tests/nextflow.voom.config
+++ b/modules/nf-core/limma/differential/tests/nextflow.voom.config
@@ -1,7 +1,5 @@
 process {
 
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: 'LIMMA_DIFFERENTIAL' {
         ext.args = { [
             "--sample_id_col sample",
diff --git a/modules/nf-core/limma/differential/tests/nextflow.voom_blocking.config b/modules/nf-core/limma/differential/tests/nextflow.voom_blocking.config
index d4e24f8538fc..253970c71197 100644
--- a/modules/nf-core/limma/differential/tests/nextflow.voom_blocking.config
+++ b/modules/nf-core/limma/differential/tests/nextflow.voom_blocking.config
@@ -1,7 +1,5 @@
 process {
 
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: 'LIMMA_DIFFERENTIAL' {
         ext.args = { [
             "--sample_id_col sample",
diff --git a/modules/nf-core/limma/differential/tests/nextflow.voom_mixed.config b/modules/nf-core/limma/differential/tests/nextflow.voom_mixed.config
index 0adc069884f8..0697731bcd99 100644
--- a/modules/nf-core/limma/differential/tests/nextflow.voom_mixed.config
+++ b/modules/nf-core/limma/differential/tests/nextflow.voom_mixed.config
@@ -1,7 +1,5 @@
 process {
 
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: 'LIMMA_DIFFERENTIAL' {
         ext.args = { [
             "--sample_id_col sample",
diff --git a/modules/nf-core/limma/differential/tests/nextflow.voom_mixed_seed.config b/modules/nf-core/limma/differential/tests/nextflow.voom_mixed_seed.config
index 2c930adec5bd..b9f357cbf4ae 100644
--- a/modules/nf-core/limma/differential/tests/nextflow.voom_mixed_seed.config
+++ b/modules/nf-core/limma/differential/tests/nextflow.voom_mixed_seed.config
@@ -1,7 +1,5 @@
 process {
 
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: 'LIMMA_DIFFERENTIAL' {
         ext.args = { [
             "--sample_id_col sample",

From 8a74021bda822b4b763e634970828feb93f5195e Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 21 Apr 2026 18:06:51 +0000
Subject: [PATCH 22/29] fix linting

---
 modules/nf-core/zip/meta.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/zip/meta.yml b/modules/nf-core/zip/meta.yml
index 4e8710219944..a0744bb0982a 100644
--- a/modules/nf-core/zip/meta.yml
+++ b/modules/nf-core/zip/meta.yml
@@ -45,7 +45,7 @@ output:
       - zip:
           type: string
           description: The name of the tool
-      - 7za --help | sed 's/.*p7zip Version //; s/(.*//':
+      - 7za i 2>&1 | grep 'p7zip Version' | sed 's/.*p7zip Version //; s/(.*//':
           type: eval
           description: The expression to obtain the version of the tool
 topics:
@@ -56,7 +56,7 @@ topics:
       - zip:
           type: string
           description: The name of the tool
-      - 7za --help | sed 's/.*p7zip Version //; s/(.*//':
+      - 7za i 2>&1 | grep 'p7zip Version' | sed 's/.*p7zip Version //; s/(.*//':
           type: eval
           description: The expression to obtain the version of the tool
 authors:

From ea900b5622e883d947b7053e2097799540780e80 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 21 Apr 2026 18:48:39 +0000
Subject: [PATCH 23/29] fix input tuple does not match tuple declaration in
 process

---
 modules/nf-core/limma/differential/tests/main.nf.test | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/limma/differential/tests/main.nf.test b/modules/nf-core/limma/differential/tests/main.nf.test
index c99914c849de..003c48e2b0da 100644
--- a/modules/nf-core/limma/differential/tests/main.nf.test
+++ b/modules/nf-core/limma/differential/tests/main.nf.test
@@ -301,7 +301,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of(['id': 'test', 'variable': 'treatment', 'reference': 'hND6', 'target': 'mCherry'])
-                        .map{tuple(it, it.variable, it.reference, it.target)}
+                        .map{tuple(it, it.variable, it.reference, it.target, it.formula, it.comparison)}
                 input[1] = Channel.of([[id:'test'],
                     file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)])
@@ -330,7 +330,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of(['id': 'test', 'variable': 'treatment', 'reference': 'hND6', 'target': 'mCherry'])
-                        .map{tuple(it, it.variable, it.reference, it.target)}
+                        .map{tuple(it, it.variable, it.reference, it.target, it.formula, it.comparison)}
                 input[1] = Channel.of([[id:'test'],
                     file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)])
@@ -359,7 +359,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of(['id': 'test', 'variable': 'treatment', 'reference': 'hND6', 'target': 'mCherry'])
-                        .map{tuple(it, it.variable, it.reference, it.target)}
+                        .map{tuple(it, it.variable, it.reference, it.target, it.formula, it.comparison)}
                 input[1] = Channel.of([[id:'test'],
                     file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)])
@@ -388,7 +388,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of(['id': 'test', 'variable': 'treatment', 'reference': 'hND6', 'target': 'mCherry'])
-                        .map{tuple(it, it.variable, it.reference, it.target)}
+                        .map{tuple(it, it.variable, it.reference, it.target, it.formula, it.comparison)}
                 input[1] = Channel.of([[id:'test'],
                     file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)])
@@ -412,7 +412,7 @@ nextflow_process {
         when {
             process {                """
                 input[0] = Channel.of(['id': 'test', 'variable': 'treatment', 'reference': 'hND6', 'target': 'mCherry'])
-                        .map{tuple(it, it.variable, it.reference, it.target)}
+                        .map{tuple(it, it.variable, it.reference, it.target, it.formula, it.comparison)}
                 input[1] = Channel.of([[id:'test'],
                     file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)])

From fdac3fc5758e2c7d135a2db4ac80e40ddf69a6dc Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Wed, 22 Apr 2026 16:27:52 +0000
Subject: [PATCH 24/29] update snapshot filterdifferentialtable

---
 .../filterdifferentialtable/tests/main.nf.test.snap  | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/custom/filterdifferentialtable/tests/main.nf.test.snap b/modules/nf-core/custom/filterdifferentialtable/tests/main.nf.test.snap
index 581f235679a3..566284db4074 100644
--- a/modules/nf-core/custom/filterdifferentialtable/tests/main.nf.test.snap
+++ b/modules/nf-core/custom/filterdifferentialtable/tests/main.nf.test.snap
@@ -27,17 +27,17 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,cb198b2ec6562ff113a18db461fabccb"
+                    "versions.yml:md5,c0d19fbbdd52d186345dd716bb94bd10"
                 ]
             },
             {
                 "CUSTOM_FILTERDIFFERENTIALTABLE": {
                     "pandas": "1.5.2",
-                    "python": "3.11.0"
+                    "python": "3.11.15"
                 }
             }
         ],
-        "timestamp": "2026-04-21T16:55:50.246656199",
+        "timestamp": "2026-04-22T16:25:27.044800112",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -71,17 +71,17 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,cb198b2ec6562ff113a18db461fabccb"
+                    "versions.yml:md5,c0d19fbbdd52d186345dd716bb94bd10"
                 ]
             },
             {
                 "CUSTOM_FILTERDIFFERENTIALTABLE": {
                     "pandas": "1.5.2",
-                    "python": "3.11.0"
+                    "python": "3.11.15"
                 }
             }
         ],
-        "timestamp": "2026-04-21T16:55:39.761118313",
+        "timestamp": "2026-04-22T16:25:17.054820398",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

From b3935a85598ba305fe92e2500020914a4028aebd Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Wed, 22 Apr 2026 16:32:20 +0000
Subject: [PATCH 25/29] fix linting

---
 .../nf-core/custom/filterdifferentialtable/meta.yml   | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/custom/filterdifferentialtable/meta.yml b/modules/nf-core/custom/filterdifferentialtable/meta.yml
index 0d2a4411706a..d21016be6dda 100644
--- a/modules/nf-core/custom/filterdifferentialtable/meta.yml
+++ b/modules/nf-core/custom/filterdifferentialtable/meta.yml
@@ -102,7 +102,14 @@ output:
         description: File containing software versions
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3750
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
 topics:
   versions:
     - versions.yml:
@@ -110,7 +117,7 @@ topics:
         description: File containing software versions
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3750
 authors:
   - "@pinin4fjords"
   - "@WackerO"

From 3fdaaa71fdce4801178712804242b170f92d943e Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Wed, 22 Apr 2026 16:49:32 +0000
Subject: [PATCH 26/29] update environment and docker container

---
 .../nf-core/custom/filterdifferentialtable/environment.yml    | 2 +-
 modules/nf-core/custom/filterdifferentialtable/main.nf        | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/custom/filterdifferentialtable/environment.yml b/modules/nf-core/custom/filterdifferentialtable/environment.yml
index cb2f96fa0797..1b23a14ce6d5 100644
--- a/modules/nf-core/custom/filterdifferentialtable/environment.yml
+++ b/modules/nf-core/custom/filterdifferentialtable/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - conda-forge::pandas=1.5.2
-  - conda-forge::python=3.11.0
+  - conda-forge::python=3.11.15
diff --git a/modules/nf-core/custom/filterdifferentialtable/main.nf b/modules/nf-core/custom/filterdifferentialtable/main.nf
index 3689da57f399..36f70c4bd218 100644
--- a/modules/nf-core/custom/filterdifferentialtable/main.nf
+++ b/modules/nf-core/custom/filterdifferentialtable/main.nf
@@ -4,8 +4,8 @@ process CUSTOM_FILTERDIFFERENTIALTABLE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4d/4d7a62daafff045d7ea7739aac6e24d495ab94512525d73bcd865f5cf27cfe0f/data' :
-        'community.wave.seqera.io/library/pandas:1.5.2--8aad09419bb2ac73' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b06950ac325030db5976f3d9c536e358eb686503af35c7e6222f86d016b3466f/data' :
+        'community.wave.seqera.io/library/pandas_python:67bda66f0cb8a241' }"
 
     input:
     tuple val(meta), path(input_file)

From bfcc2af4eb4aa85daac5b80df3d43b98e31e88a5 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Wed, 22 Apr 2026 16:52:41 +0000
Subject: [PATCH 27/29] update snapshot

---
 modules/nf-core/limma/differential/tests/main.nf.test     | 2 +-
 .../nf-core/limma/differential/tests/main.nf.test.snap    | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/limma/differential/tests/main.nf.test b/modules/nf-core/limma/differential/tests/main.nf.test
index 003c48e2b0da..02b235145252 100644
--- a/modules/nf-core/limma/differential/tests/main.nf.test
+++ b/modules/nf-core/limma/differential/tests/main.nf.test
@@ -313,7 +313,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out.model, process.out.versions).match() },
-                { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-4.89014922224241") },
+                { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-4.89014922224") },
                 { assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.77922") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") },
                 { assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000059991\t4.52751370160052") }
diff --git a/modules/nf-core/limma/differential/tests/main.nf.test.snap b/modules/nf-core/limma/differential/tests/main.nf.test.snap
index 75e1c364d086..9c3909b9cffd 100644
--- a/modules/nf-core/limma/differential/tests/main.nf.test.snap
+++ b/modules/nf-core/limma/differential/tests/main.nf.test.snap
@@ -31,17 +31,17 @@
                         "reference": "hND6",
                         "target": "mCherry"
                     },
-                    "test.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d"
+                    "test.limma.model.txt:md5,cb9d919594a83c8d15e3693bd599a0bb"
                 ]
             ],
             [
                 "versions.yml:md5,88a6e42d753077edab8daf829cd4d943"
             ]
         ],
-        "timestamp": "2024-10-31T12:35:52.20676",
+        "timestamp": "2026-04-22T16:52:14.678632369",
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
         }
     },
     "test_limma_differential - voom": {

From 77d3dcdb9735f0ada44e3f5437a47d4731bc860e Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Wed, 22 Apr 2026 17:13:14 +0000
Subject: [PATCH 28/29] fix linting

---
 modules/nf-core/custom/filterdifferentialtable/meta.yml | 7 -------
 modules/nf-core/limma/differential/main.nf              | 2 +-
 2 files changed, 1 insertion(+), 8 deletions(-)

diff --git a/modules/nf-core/custom/filterdifferentialtable/meta.yml b/modules/nf-core/custom/filterdifferentialtable/meta.yml
index d21016be6dda..50394aeb3be4 100644
--- a/modules/nf-core/custom/filterdifferentialtable/meta.yml
+++ b/modules/nf-core/custom/filterdifferentialtable/meta.yml
@@ -96,13 +96,6 @@ output:
           pattern: "*_filtered_down.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475
-  versions_customfilterdifferentialtable:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750
   versions:
     - versions.yml:
         type: file
diff --git a/modules/nf-core/limma/differential/main.nf b/modules/nf-core/limma/differential/main.nf
index 0d40e8654c2e..0fa81751a966 100644
--- a/modules/nf-core/limma/differential/main.nf
+++ b/modules/nf-core/limma/differential/main.nf
@@ -18,7 +18,7 @@ process LIMMA_DIFFERENTIAL {
     tuple val(meta), path("*.limma.model.txt")            , emit: model
     tuple val(meta), path("*.R_sessionInfo.log")          , emit: session_info
     tuple val(meta), path("*.normalised_counts.tsv")      , emit: normalised_counts, optional: true
-    path "versions.yml"                                   , emit: versions
+    path "versions.yml"                                   , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

From 93485ab3c786582c75b9618dc3d340a238506d73 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Wed, 22 Apr 2026 17:16:06 +0000
Subject: [PATCH 29/29] fix litngin

---
 modules/nf-core/limma/differential/meta.yml | 32 ++++++++++++---------
 1 file changed, 19 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/limma/differential/meta.yml b/modules/nf-core/limma/differential/meta.yml
index 175f555262a4..20a85736d7af 100644
--- a/modules/nf-core/limma/differential/meta.yml
+++ b/modules/nf-core/limma/differential/meta.yml
@@ -12,7 +12,8 @@ tools:
       documentation: "https://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf"
       tool_dev_url: https://github.com/cran/limma""
       doi: "10.18129/B9.bioc.limma"
-      licence: ["LGPL >=3"]
+      licence:
+        - "LGPL >=3"
       identifier: biotools:limma
 input:
   - - meta:
@@ -39,12 +40,12 @@ input:
           should be used to derive the target samples
     - formula:
         type: string
-        description: (Optional, requires comparison if used) R formula string used for
-          modeling, e.g. '~ treatment'.
+        description: (Optional, requires comparison if used) R formula string used
+          for modeling, e.g. '~ treatment'.
     - comparison:
         type: string
-        description: (Optional, mandatory if formula is used) Literal string passed
-          to `limma::makeContrasts`, e.g. 'treatmentmCherry'.
+        description: (Optional, mandatory if formula is used) Literal string
+          passed to `limma::makeContrasts`, e.g. 'treatmentmCherry'.
   - - meta2:
         type: map
         description: |
@@ -71,11 +72,11 @@ output:
             '--blocking_variable $meta.blocking'.
       - "*.limma.results.tsv":
           type: file
-          description: TSV-format table of differential expression information as output
-            by Limma
+          description: TSV-format table of differential expression information as
+            output by Limma
           pattern: "*.limma.results.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   md_plot:
     - - meta:
           type: map
@@ -115,7 +116,7 @@ output:
           description: TXT-format limma model
           pattern: "*.limma.model.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   session_info:
     - - meta:
           type: map
@@ -139,18 +140,23 @@ output:
             '--blocking_variable $meta.blocking'.
       - "*.normalised_counts.tsv":
           type: file
-          description: normalised TSV format expression matrix with probes by row and
-            samples by column
+          description: normalised TSV format expression matrix with probes by row
+            and samples by column
           pattern: "*.normalised_counts.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   versions:
     - versions.yml:
         type: file
         description: File containing software versions
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3750
+topics:
+  versions:
+    - versions.yml:
+        type: string
+        description: The name of the process
 authors:
   - "@pinin4fjords"
 maintainers: