Topics

CHANGELOG.md

@@ -9,6 +9,7 @@ Initial release of nf-core/scdownstream, created with the [nf-core](https://nf-c
 
 ### `Added`
 
+- Use topics for software versioning [[#252](https://github.com/nf-core/scdownstream/pull/252)]
 - Added `singleR` module for automated cell type annotation.
 
 ### `Fixed`

modules.json

@@ -18,7 +18,8 @@
                     "cellbender/merge": {
                         "branch": "master",
                         "git_sha": "380cb90926b8c28558cb11479da5ff45bc4f1c5d",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/cellbender/merge/cellbender-merge.diff"
                     },
                     "cellbender/removebackground": {
                         "branch": "master",

modules/local/adata/entropy/main.nf

@@ -17,7 +17,7 @@ process ADATA_ENTROPY {
     path "${prefix}.pkl"                   , emit: obs
     path "${prefix}.png"                   , emit: plots, optional: true
     path "${prefix}_mqc.json"              , emit: multiqc_files, optional: true
-    path "versions.yml"                    , emit: versions
+    path "versions.yml"                    , emit: versions, topic: versions
 
     script:
     prefix = task.ext.prefix ?: "${meta.id}_entropy"

modules/local/adata/extend/main.nf

@@ -21,8 +21,8 @@ process ADATA_EXTEND {
 
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
-    tuple val(meta), path("*.csv"), emit: metadata
-    path "versions.yml", emit: versions
+    tuple val(meta), path("*.csv") , emit: metadata
+    path "versions.yml"            , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/adata/merge/main.nf

@@ -17,7 +17,7 @@ process ADATA_MERGE {
     tuple val(meta), path("*_inner.h5ad")    , emit: inner
     tuple val(meta), path("*_integrate.h5ad"), emit: integrate
     path "gene_intersection.pkl"             , emit: intersect_genes
-    path "versions.yml"                      , emit: versions
+    path "versions.yml"                      , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/adata/mergeembeddings/main.nf

@@ -12,9 +12,9 @@ process ADATA_MERGEEMBEDDINGS {
 
     output:
     tuple val(meta), path("${prefix}.h5ad"), emit: h5ad
-    path ("${prefix}.pkl"), emit: obs, optional: true
-    path ("X_${prefix}.pkl"), emit: obsm
-    path "versions.yml", emit: versions
+    path ("${prefix}.pkl")                 , emit: obs, optional: true
+    path ("X_${prefix}.pkl")               , emit: obsm
+    path "versions.yml"                    , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/adata/mygene/main.nf

@@ -12,7 +12,7 @@ process ADATA_MYGENE {
 
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
-    path "versions.yml"            , emit: versions
+    path "versions.yml"            , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/adata/prepcellxgene/main.nf

@@ -12,7 +12,7 @@ process ADATA_PREPCELLXGENE {
 
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
-    path "versions.yml", emit: versions
+    path "versions.yml"            , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/adata/readcsv/main.nf

@@ -12,7 +12,7 @@ process ADATA_READCSV {
 
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
-    path "versions.yml", emit: versions
+    path "versions.yml"            , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/adata/readrds/main.nf

@@ -12,7 +12,7 @@ process ADATA_READRDS {
 
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
-    path "versions.yml"            , emit: versions
+    path "versions.yml"            , emit: versions, topic: versions
 
     script:
     prefix = task.ext.prefix ?: "${meta.id}"

modules/local/adata/setindex/main.nf

@@ -14,7 +14,7 @@ process ADATA_SETINDEX {
 
     output:
     tuple val(meta), path("${prefix}.h5ad"), emit: h5ad
-    path "versions.yml", emit: versions
+    path "versions.yml"                    , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/adata/splitcol/main.nf

@@ -13,7 +13,7 @@ process ADATA_SPLITCOL {
 
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
-    path "versions.yml", emit: versions
+    path "versions.yml"            , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/adata/splitembeddings/main.nf

@@ -13,7 +13,7 @@ process ADATA_SPLITEMBEDDINGS {
 
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
-    path "versions.yml", emit: versions
+    path "versions.yml"            , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/adata/tords/main.nf

@@ -13,7 +13,7 @@ process ADATA_TORDS {
 
     output:
     tuple val(meta), path("*.rds"), emit: rds
-    path "versions.yml"           , emit: versions
+    path "versions.yml"           , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/adata/unify/main.nf

@@ -20,7 +20,7 @@ process ADATA_UNIFY {
 
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
-    path "versions.yml", emit: versions
+    path "versions.yml"            , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/adata/upsetgenes/main.nf

@@ -12,8 +12,8 @@ process ADATA_UPSETGENES {
 
     output:
     tuple val(meta), path("*.png"), emit: plot, optional: true
-    path ("*_mqc.json"), emit: multiqc_files, optional: true
-    path "versions.yml", emit: versions
+    path ("*_mqc.json")           , emit: multiqc_files, optional: true
+    path "versions.yml"           , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/celda/decontx/main.nf

@@ -15,7 +15,7 @@ process CELDA_DECONTX {
 
     output:
     tuple val(meta), path("${prefix}.h5ad"), emit: h5ad
-    path "versions.yml"            , emit: versions
+    path "versions.yml"                    , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/celldex/fetchreference/main.nf

@@ -13,7 +13,7 @@ process CELLDEX_FETCHREFERENCE {
 
     output:
     tuple val(meta), path("${prefix}.tar"), emit: tar
-    path "versions.yml", emit: versions
+    path "versions.yml"                   , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/celltypes/celltypist/main.nf

@@ -13,8 +13,8 @@ process CELLTYPES_CELLTYPIST {
 
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
-    tuple val(meta), path("*.pkl"), emit: obs
-    path "versions.yml", emit: versions
+    tuple val(meta), path("*.pkl") , emit: obs
+    path "versions.yml"            , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/celltypes/singler/main.nf

@@ -15,7 +15,7 @@ process CELLTYPES_SINGLER {
     tuple val(meta), path("*.csv")             , emit: obs
     tuple val(meta), path("*_distribution.pdf"), emit: distribution
     tuple val(meta), path("*_heatmap.pdf")     , emit: heatmap
-    path "versions.yml"                        , emit: versions
+    path "versions.yml"                        , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/custom/collectsizes/main.nf

@@ -13,7 +13,7 @@ process CUSTOM_COLLECTSIZES {
     output:
     tuple val(meta), path("*.tsv"), emit: tsv
     path("*_mqc.json")            , emit: multiqc_files
-    path "versions.yml"           , emit: versions
+    path "versions.yml"           , emit: versions, topic: versions
 
     script:
     prefix = task.ext.prefix ?: "${meta.id}"

modules/local/doublet_detection/doublet_removal/main.nf

@@ -14,7 +14,7 @@ process DOUBLET_REMOVAL {
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
     path("*_mqc.json")             , emit: multiqc_files, optional: true
-    path "versions.yml"            , emit: versions
+    path "versions.yml"            , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/doublet_detection/scds/main.nf

@@ -9,8 +9,8 @@ process SCDS {
 
     output:
     tuple val(meta), path("${prefix}.h5ad"), emit: h5ad
-    tuple val(meta), path("${prefix}.csv"), emit: predictions
-    path "versions.yml", emit: versions
+    tuple val(meta), path("${prefix}.csv") , emit: predictions
+    path "versions.yml"                    , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/hugounifier/apply/main.nf

@@ -12,23 +12,17 @@ process HUGOUNIFIER_APPLY {
 
     output:
     tuple val(meta), path("${prefix}.h5ad"), emit: h5ad
-    path ("versions.yml")                  , emit: versions
+    tuple val("${task.process}"), val('hugo-unifier'), eval('hugo-unifier --version | grep -oP "(?<=version )[\\d.]+"'), emit: versions_hugo_unifier, topic: versions
 
     script:
     prefix = task.ext.prefix ?: meta.id
     """
     hugo-unifier apply -i ${h5ad} -c ${changes} -o ${prefix}.h5ad
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hugo-unifier: \$(hugo-unifier --version | grep -oP '(?<=version )[\\d.]+')
-    END_VERSIONS
     """
 
     stub:
     prefix = task.ext.prefix ?: meta.id
     """
     touch ${prefix}.h5ad
-    touch versions.yml
     """
 }

modules/local/hugounifier/apply/tests/main.nf.test

@@ -52,7 +52,7 @@ nextflow_process {
                 assert obs.rownames.size() > 0
             }
             assert snapshot(
-                path(process.out.versions[0]).yaml,
+                process.out.versions,
                 adata.yaml
             ).match()
         }

modules/local/hugounifier/apply/tests/main.nf.test.snap

@@ -11,7 +11,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    [
+                        "HUGOUNIFIER_APPLY",
+                        "hugo-unifier",
+                        "0.3.1"
+                    ]
                 ],
                 "h5ad": [
                     [
@@ -21,24 +25,24 @@
                         "test_hugounifier.h5ad:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "versions_hugo_unifier": [
+                    [
+                        "HUGOUNIFIER_APPLY",
+                        "hugo-unifier",
+                        "0.3.1"
+                    ]
                 ]
             }
         ],
-        "timestamp": "2026-01-10T23:17:20.422385507",
+        "timestamp": "2026-04-01T21:30:55.233019",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
         }
     },
     "Should run without failures": {
         "content": [
-            {
-                "HUGOUNIFIER_APPLY": {
-                    "hugo-unifier": "0.3.1"
-                }
-            },
+            null,
             {
                 "n_obs": 12940,
                 "n_vars": 9887,
@@ -74,10 +78,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-29T14:29:56.746430632",
+        "timestamp": "2026-04-01T21:30:42.63053",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.2"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
         }
     }
 }

modules/local/hugounifier/get/main.nf

@@ -12,18 +12,13 @@ process HUGOUNIFIER_GET {
 
     output:
     tuple val(meta), path("${meta.id}/*.csv"), emit: changes
-    path ("versions.yml")                    , emit: versions
+    tuple val("${task.process}"), val('hugo-unifier'), eval('hugo-unifier --version | grep -oP "(?<=version )[\\d.]+"'), emit: versions_hugo_unifier, topic: versions
 
     script:
     def namedFiles = [[names].flatten(), [h5ads].flatten()].transpose()
     def input = namedFiles.collect { name, h5ad -> "-i ${name}:${h5ad}" }.join(' ')
     """
     hugo-unifier get -o ${meta.id} ${input}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hugo-unifier: \$(hugo-unifier --version | grep -oP '(?<=version )[\\d.]+')
-    END_VERSIONS
     """
 
     stub:
@@ -33,7 +28,5 @@ process HUGOUNIFIER_GET {
     for name in ${names.join(' ')}; do
         touch ${meta.id}/\${name}.csv
     done
-
-    touch versions.yml
     """
 }

modules/local/hugounifier/get/tests/main.nf.test

@@ -38,7 +38,7 @@ nextflow_process {
                 assert columnNames == ["action", "symbol", "new", "reason"]
             }
             assert snapshot(
-                path(process.out.versions[0]).yaml
+                process.out.versions
             ).match()
         }