Migrate missing nf-core/differentialabundance modules to Seqera containers

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':
-        'quay.io/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)

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':
-        'quay.io/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)

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':
-        'quay.io/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)

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

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' :
-        'quay.io/biocontainers/pandas:1.5.2' }"
+        '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)

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
@@ -89,25 +91,26 @@ 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
 topics:
   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"

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"

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' :
-        'quay.io/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)

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

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' :
-        'quay.io/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)
@@ -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

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"

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

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:

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)])
@@ -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") }
@@ -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)])