scanpy-related local modules use harmonized Seqera image

modules/local/adata/entropy/environment.yml

@@ -2,5 +2,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - conda-forge::python=3.13.12
   - conda-forge::pyyaml=6.0.3
-  - conda-forge::scanpy=1.11.5
+  - conda-forge::scanpy=1.12

modules/local/adata/entropy/main.nf

@@ -4,8 +4,8 @@ process ADATA_ENTROPY {
 
     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/fd/fd27aeaf160eaba9a58c029e08f1da74051aa292c2fb043a5dd68fddcde3af93/data':
-        'community.wave.seqera.io/library/pyyaml_scanpy:3c9e9f631f45553d' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/45/45339bf761a2cf0cdb058492bc37f3df8b05b363731d491d1d3a14e9ba0b8f55/data':
+        'community.wave.seqera.io/library/harmonypy_anndata_leidenalg_numpy_pruned:43066d5f86f18261' }"
 
     input:
     tuple val(meta), path(h5ad)
@@ -22,6 +22,7 @@ process ADATA_ENTROPY {
     script:
     prefix = task.ext.prefix ?: "${meta.id}_entropy"
     plot_basis = task.ext.plot_basis ?: null
+    args = task.ext.args ?: ''
     template 'entropy.py'
 
     stub:

modules/local/adata/entropy/templates/entropy.py

@@ -5,6 +5,8 @@
 import json
 import base64
 import yaml
+import argparse
+import shlex
 
 os.environ["NUMBA_CACHE_DIR"] = "./tmp/numba"
 os.environ["MPLCONFIGDIR"] = "./tmp/matplotlib"
@@ -19,6 +21,11 @@
 entropy_col = "${entropy_col}"
 prefix = "${prefix}"
 adata = sc.read_h5ad("${h5ad}", backed='r')
+args = "${args}"
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--decimals", type=int, default=None)
+params = parser.parse_args(shlex.split(args))
 
 def entropy_of_group(group):
     counts = group.value_counts(normalize=True)
@@ -30,8 +37,8 @@ def entropy_of_group(group):
 colname = "${meta.id}:entropy"
 adata.obs[colname] = adata.obs[group_col].map(entropies).astype(float) / np.log2(n_unique)
 
-# Round to prevent hash inconsistencies
-adata.obs[colname] = adata.obs[colname].round(3)
+if params.decimals is not None:
+    adata.obs[colname] = adata.obs[colname].round(params.decimals)
 
 adata.obs[[colname]].to_pickle(f"{prefix}.pkl")
 adata.write_h5ad(f"{prefix}.h5ad")

modules/local/adata/entropy/tests/main.nf.test

@@ -6,51 +6,21 @@ nextflow_process {
     tag "modules"
     tag "modules_local"
 
-        setup {
-        run("SCANPY_PCA") {
-            script "modules/local/scanpy/pca/main.nf"
-            process {
-                """
-                input[0] = channel.of([
-                        [ id: 'test' ],
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/h5ad/combined_filtered_matrix.h5ad', checkIfExists: true)
-                    ]
-                )
-                input[1] = "X_pca"
-                """
-            }
-        }
-        run("SCANPY_NEIGHBORS") {
-            script "modules/local/scanpy/neighbors/main.nf"
-            process {
-                """
-                input[0] = SCANPY_PCA.out.h5ad
-                input[1] = "X_pca"
-                """
-            }
-        }
-        run("SCANPY_LEIDEN") {
-            script "modules/local/scanpy/leiden/main.nf"
-            process {
-                """
-                input[0] = SCANPY_NEIGHBORS.out.h5ad
-                input[1] = 1.0
-                input[2] = "leiden"
-                input[3] = false
-                """
-            }
-        }
-    }
-
     test("Should run without failures") {
 
+        config './nextflow.config'
+
         when {
             params {
                 outdir = "$outputDir"
             }
             process {
                 """
-                input[0] = SCANPY_LEIDEN.out.h5ad
+                input[0] = channel.of([
+                        [ id: 'test' ],
+                        file(params.pipelines_testdata_base_path + '/pbmc/combined_filtered_pca.h5ad', checkIfExists: true)
+                    ]
+                )
                 input[1] = 'leiden'
                 input[2] = 'sample'
                 """
@@ -76,7 +46,11 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = SCANPY_LEIDEN.out.h5ad
+                input[0] = channel.of([
+                        [ id: 'test' ],
+                        file(params.pipelines_testdata_base_path + '/pbmc/combined_filtered_pca.h5ad', checkIfExists: true)
+                    ]
+                )
                 input[1] = 'leiden'
                 input[2] = 'sample'
                 """

modules/local/adata/entropy/tests/main.nf.test.snap

@@ -44,11 +44,11 @@
                 ]
             }
         ],
+        "timestamp": "2025-06-22T15:55:46.390569411",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.3"
-        },
-        "timestamp": "2025-06-22T15:55:46.390569411"
+        }
     },
     "Should run without failures": {
         "content": [
@@ -58,11 +58,11 @@
                         {
                             "id": "test"
                         },
-                        "test_entropy.h5ad:md5,0ddf3491267da3afcd7d49bfb601bc39"
+                        "test_entropy.h5ad:md5,f874063c56014bfe710f56e18e52b74f"
                     ]
                 ],
                 "1": [
-                    "test_entropy.pkl:md5,0cce150308d3fd0a6b08795a68fea389"
+                    "test_entropy.pkl:md5,43f99ffbaf5232c2a0841c2b3888bfd9"
                 ],
                 "2": [
 
@@ -71,34 +71,34 @@
 
                 ],
                 "4": [
-                    "versions.yml:md5,fec1a6bc52548627507fb8d06e60da52"
+                    "versions.yml:md5,06c3be8b97dfd251b6aef3221b56d5fc"
                 ],
                 "h5ad": [
                     [
                         {
                             "id": "test"
                         },
-                        "test_entropy.h5ad:md5,0ddf3491267da3afcd7d49bfb601bc39"
+                        "test_entropy.h5ad:md5,f874063c56014bfe710f56e18e52b74f"
                     ]
                 ],
                 "multiqc_files": [
 
                 ],
                 "obs": [
-                    "test_entropy.pkl:md5,0cce150308d3fd0a6b08795a68fea389"
+                    "test_entropy.pkl:md5,43f99ffbaf5232c2a0841c2b3888bfd9"
                 ],
                 "plots": [
 
                 ],
                 "versions": [
-                    "versions.yml:md5,fec1a6bc52548627507fb8d06e60da52"
+                    "versions.yml:md5,06c3be8b97dfd251b6aef3221b56d5fc"
                 ]
             }
         ],
+        "timestamp": "2026-03-22T09:52:42.901052235",
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.4",
             "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-25T17:05:22.295034358"
+        }
     }
 }

modules/local/adata/entropy/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: ADATA_ENTROPY {
+        ext.args = '--decimals 3'
+    }
+}

modules/local/adata/extend/environment.yml

@@ -2,5 +2,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::anndata=0.12.7
+  - conda-forge::python=3.13.12
+  - conda-forge::anndata=0.12.10
   - conda-forge::pyyaml=6.0.3

modules/local/adata/extend/main.nf

@@ -4,8 +4,8 @@ process ADATA_EXTEND {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/76/7612a78c6f49cfbeebf84c444ad314bf86da041588f3b0f14951e462e18a9228/data'
-        : 'community.wave.seqera.io/library/anndata_pyyaml:82c6914e861435f7'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/45/45339bf761a2cf0cdb058492bc37f3df8b05b363731d491d1d3a14e9ba0b8f55/data'
+        : 'community.wave.seqera.io/library/harmonypy_anndata_leidenalg_numpy_pruned:43066d5f86f18261'}"
 
     input:
     tuple (

modules/local/adata/extend/tests/main.nf.test.snap

@@ -19,7 +19,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,820747e56d08a1eae6b8dfb082f347a0"
+                    "versions.yml:md5,b2a073150918c118c3858cf4e82145f7"
                 ],
                 "h5ad": [
                     [
@@ -38,15 +38,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,820747e56d08a1eae6b8dfb082f347a0"
+                    "versions.yml:md5,b2a073150918c118c3858cf4e82145f7"
                 ]
             }
         ],
+        "timestamp": "2026-03-16T15:14:17.984419949",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2026-01-16T22:00:29.120765286"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "Should extend with obsm data": {
         "content": [
@@ -68,7 +68,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,820747e56d08a1eae6b8dfb082f347a0"
+                    "versions.yml:md5,b2a073150918c118c3858cf4e82145f7"
                 ],
                 "h5ad": [
                     [
@@ -87,15 +87,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,820747e56d08a1eae6b8dfb082f347a0"
+                    "versions.yml:md5,b2a073150918c118c3858cf4e82145f7"
                 ]
             }
         ],
+        "timestamp": "2026-03-16T15:13:53.551305616",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2026-01-16T22:00:13.25388026"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "Should extend with uns data": {
         "content": [
@@ -117,7 +117,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,820747e56d08a1eae6b8dfb082f347a0"
+                    "versions.yml:md5,b2a073150918c118c3858cf4e82145f7"
                 ],
                 "h5ad": [
                     [
@@ -136,15 +136,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,820747e56d08a1eae6b8dfb082f347a0"
+                    "versions.yml:md5,b2a073150918c118c3858cf4e82145f7"
                 ]
             }
         ],
+        "timestamp": "2026-03-16T15:14:39.805580912",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2026-01-16T22:00:44.610008207"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "Should extend with obs data": {
         "content": [
@@ -166,7 +166,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,820747e56d08a1eae6b8dfb082f347a0"
+                    "versions.yml:md5,b2a073150918c118c3858cf4e82145f7"
                 ],
                 "h5ad": [
                     [
@@ -185,15 +185,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,820747e56d08a1eae6b8dfb082f347a0"
+                    "versions.yml:md5,b2a073150918c118c3858cf4e82145f7"
                 ]
             }
         ],
+        "timestamp": "2026-03-16T15:13:30.793377663",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2026-01-16T21:59:57.879659481"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "Should run without failures - stub": {
         "content": [
@@ -238,11 +238,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-01-16T22:01:11.948835963",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
-        },
-        "timestamp": "2026-01-16T22:01:11.948835963"
+        }
     },
     "Should run with no extensions": {
         "content": [
@@ -264,7 +264,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,820747e56d08a1eae6b8dfb082f347a0"
+                    "versions.yml:md5,b2a073150918c118c3858cf4e82145f7"
                 ],
                 "h5ad": [
                     [
@@ -283,14 +283,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,820747e56d08a1eae6b8dfb082f347a0"
+                    "versions.yml:md5,b2a073150918c118c3858cf4e82145f7"
                 ]
             }
         ],
+        "timestamp": "2026-03-16T15:14:59.60059937",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2026-01-16T22:00:59.998455502"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }

modules/local/adata/merge/environment.yml

@@ -2,5 +2,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - conda-forge::python=3.13.12
   - conda-forge::pyyaml=6.0.3
-  - conda-forge::scanpy=1.11.5
+  - conda-forge::scanpy=1.12