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nf-core · Jun 11, 2024 · 3981565 · 3981565
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diff --git a/README.md b/README.md
@@ -26,22 +26,22 @@
 Not all of the steps shown in the metromap have already been implemented, as this pipeline is still under development. However, the following steps are already functional:
 
 1. Per-dataset preprocessing
-    1. Convert all RDS files to h5ad format
-    2. Present QC for raw counts ([`MultiQC`](http://multiqc.info/))
-    3. Apply user-defined QC filters
-    4. Remove ambient RNA
-        - [decontX](https://bioconductor.org/packages/release/bioc/html/decontX.html)
-    5. Doublet detection
-        - [SOLO](https://docs.scvi-tools.org/en/stable/user_guide/models/solo.html)
+   1. Convert all RDS files to h5ad format
+   2. Present QC for raw counts ([`MultiQC`](http://multiqc.info/))
+   3. Apply user-defined QC filters
+   4. Remove ambient RNA
+      - [decontX](https://bioconductor.org/packages/release/bioc/html/decontX.html)
+   5. Doublet detection
+      - [SOLO](https://docs.scvi-tools.org/en/stable/user_guide/models/solo.html)
 2. Dataset aggregation
-    1. Merge into a single h5ad file
-    2. Present QC for merged counts ([`MultiQC`](http://multiqc.info/))
-    3. Integration
-        - [scVI](https://docs.scvi-tools.org/en/stable/user_guide/models/scvi.html)
-        - [scANVI](https://docs.scvi-tools.org/en/stable/user_guide/models/scanvi.html)
+   1. Merge into a single h5ad file
+   2. Present QC for merged counts ([`MultiQC`](http://multiqc.info/))
+   3. Integration
+      - [scVI](https://docs.scvi-tools.org/en/stable/user_guide/models/scvi.html)
+      - [scANVI](https://docs.scvi-tools.org/en/stable/user_guide/models/scanvi.html)
 3. Clustering and dimensionality reduction
-    1. [Leiden clustering](https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.leiden.html)
-    2. [UMAP](https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.umap.html)
+   1. [Leiden clustering](https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.leiden.html)
+   2. [UMAP](https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.umap.html)
 
 ## Usage
 

diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -11,9 +11,7 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Dataset name must be provided and cannot contain spaces",
-                "meta": [
-                    "id"
-                ]
+                "meta": ["id"]
             },
             "file": {
                 "type": "string",
@@ -43,9 +41,6 @@
                 "meta": ["unknown_label"]
             }
         },
-        "required": [
-            "dataset",
-            "file"
-        ]
+        "required": ["dataset", "file"]
     }
 }
diff --git a/modules.json b/modules.json
@@ -8,9 +8,7 @@
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             },
@@ -19,26 +17,20 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/modules/local/adata/extend/environment.yml b/modules/local/adata/extend/environment.yml
@@ -1,6 +1,6 @@
 name: adata_extend
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- conda-forge::anndata=0.10.7
+  - conda-forge::anndata=0.10.7
diff --git a/modules/local/adata/merge/environment.yml b/modules/local/adata/merge/environment.yml
@@ -1,6 +1,6 @@
 name: adata_merge
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- conda-forge::scanpy=1.10.1
+  - conda-forge::scanpy=1.10.1
diff --git a/modules/local/adata/readrds/environment.yml b/modules/local/adata/readrds/environment.yml
@@ -1,8 +1,8 @@
-name:  adata_readrds
+name: adata_readrds
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- bioconda::anndata2ri=1.3.1
-- conda-forge::anndata=0.10.7
-- conda-forge::r-seurat=5.0.3
+  - bioconda::anndata2ri=1.3.1
+  - conda-forge::anndata=0.10.7
+  - conda-forge::r-seurat=5.0.3
diff --git a/modules/local/adata/tords/environment.yml b/modules/local/adata/tords/environment.yml
@@ -1,8 +1,8 @@
-name:  adata_tords
+name: adata_tords
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- bioconda::anndata2ri=1.3.1
-- conda-forge::anndata=0.10.7
-- conda-forge::r-seurat=5.0.3
+  - bioconda::anndata2ri=1.3.1
+  - conda-forge::anndata=0.10.7
+  - conda-forge::r-seurat=5.0.3
diff --git a/modules/local/adata/unify/environment.yml b/modules/local/adata/unify/environment.yml
@@ -1,6 +1,6 @@
 name: adata_unify
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- conda-forge::anndata=0.10.7
+  - conda-forge::anndata=0.10.7
diff --git a/modules/local/adata/upsetgenes/environment.yml b/modules/local/adata/upsetgenes/environment.yml
@@ -1,7 +1,7 @@
 name: adata_upsetgenes
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- conda-forge::scanpy=1.10.1
-- conda-forge::upsetplot=0.9.0
+  - conda-forge::scanpy=1.10.1
+  - conda-forge::upsetplot=0.9.0
diff --git a/modules/local/celda/decontx/environment.yml b/modules/local/celda/decontx/environment.yml
@@ -1,8 +1,8 @@
 name: celda_decontx
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- bioconda::anndata2ri=1.3.1
-- bioconda::bioconductor-celda=1.18.1
-- conda-forge::anndata=0.10.7
+  - bioconda::anndata2ri=1.3.1
+  - bioconda::bioconductor-celda=1.18.1
+  - conda-forge::anndata=0.10.7
diff --git a/modules/local/scanpy/leiden/environment.yml b/modules/local/scanpy/leiden/environment.yml
@@ -1,8 +1,8 @@
 name: scanpy_leiden
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- conda-forge::leidenalg=0.10.2
-- conda-forge::python-igraph=0.11.4
-- conda-forge::scanpy=1.10.1
+  - conda-forge::leidenalg=0.10.2
+  - conda-forge::python-igraph=0.11.4
+  - conda-forge::scanpy=1.10.1
diff --git a/modules/local/scanpy/neighbors/environment.yml b/modules/local/scanpy/neighbors/environment.yml
@@ -1,7 +1,7 @@
 name: scanpy_neighbors
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- conda-forge::python-igraph=0.11.4
-- conda-forge::scanpy=1.10.1
+  - conda-forge::python-igraph=0.11.4
+  - conda-forge::scanpy=1.10.1
diff --git a/modules/local/scanpy/plotqc/environment.yml b/modules/local/scanpy/plotqc/environment.yml
@@ -1,6 +1,6 @@
 name: scanpy_plotqc
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- conda-forge::scanpy=1.10.1
+  - conda-forge::scanpy=1.10.1
diff --git a/modules/local/scanpy/umap/environment.yml b/modules/local/scanpy/umap/environment.yml
@@ -1,6 +1,6 @@
 name: scanpy_umap
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- conda-forge::scanpy=1.10.1
+  - conda-forge::scanpy=1.10.1
diff --git a/modules/local/scvitools/scanvi/environment.yml b/modules/local/scvitools/scanvi/environment.yml
@@ -1,6 +1,6 @@
 name: scvitools_scanvi
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- conda-forge::scvi-tools=1.1.2
+  - conda-forge::scvi-tools=1.1.2
diff --git a/modules/local/scvitools/scvi/environment.yml b/modules/local/scvitools/scvi/environment.yml
@@ -1,6 +1,6 @@
 name: scvitools_scvi
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- conda-forge::scvi-tools=1.1.2
+  - conda-forge::scvi-tools=1.1.2
diff --git a/modules/local/scvitools/solo/environment.yml b/modules/local/scvitools/solo/environment.yml
@@ -1,6 +1,6 @@
 name: scvitools_solo
 channels:
-- conda-forge
-- bioconda
+  - conda-forge
+  - bioconda
 dependencies:
-- conda-forge::scvi-tools=1.1.2
+  - conda-forge::scvi-tools=1.1.2
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,10 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": [
-                "input",
-                "outdir"
-            ],
+            "required": ["input", "outdir"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -54,17 +51,13 @@
                 "ambient_removal": {
                     "type": "string",
                     "default": "decontx",
-                    "enum": [
-                        "decontx"
-                    ],
+                    "enum": ["decontx"],
                     "description": "Specify the tool to use for ambient RNA removal"
                 },
                 "doublet_detection": {
                     "type": "string",
                     "default": "solo",
-                    "enum": [
-                        "solo"
-                    ],
+                    "enum": ["solo"],
                     "description": "Specify the tool to use for doublet detection"
                 },
                 "integration_methods": {
@@ -191,14 +184,7 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": [
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ],
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
                 },
                 "email_on_fail": {