biopipen 0.7.0__py3-none-any.whl → 0.8.0__py3-none-any.whl

biopipen/ns/scrna_metabolic_landscape.py

@@ -5,211 +5,13 @@ from typing import Type
 
 from diot import Diot
 from datar.tibble import tibble
-from pipen_cli_run import Pipeline, process
+from pipen_args import ProcGroup
 
 from ..core.config import config
 from ..core.proc import Proc
 
-DEFAULT_OPTS = Diot(
-    metafile=None,
-    is_seurat=None,
-    gmtfile=None,
-    grouping=None,
-    grouping_prefix="",
-    subsetting=None,
-    subsetting_prefix=None,
-    subsetting_comparison={},
-    mutaters=None,
-    ncores=config.misc.ncores,
-)
-
-
-class MetabolicPathwayActivity(Proc):
-    """Pathway activities for each group
-
-    Requires:
-        - name: r-scater
-        check: |
-            {{proc.lang}} <(echo "library(scater)")
-        - name: r-reshape2
-        check: |
-            {{proc.lang}} <(echo "library(reshape2)")
-        - name: r-rcolorbrewer
-        check: |
-            {{proc.lang}} <(echo "library(RColorBrewer)")
-        - name: r-ggplot2
-        check: |
-            {{proc.lang}} <(echo "library(ggplot2)")
-        - name: r-ggprism
-        check: |
-            {{proc.lang}} <(echo "library(ggprism)")
-        - name: r-complexheatmap
-        check: |
-            {{proc.lang}} <(echo "library(ComplexHeatmap)")
-        - name: r-parallel
-        check: |
-            {{proc.lang}} <(echo "library(parallel)")
-    """
-    input = "sobjfile:file"
-    output = "outdir:dir:{{in.sobjfile | stem}}.pathwayactivity"
-    envs = {
-        "ntimes": 5000,
-        "ncores": config.misc.ncores,
-        "heatmap_devpars": {},
-        "violin_devpars": {},
-        "gmtfile": None,
-        "grouping": None,
-        "grouping_prefix": "",
-        "subsetting": None,
-        "subsetting_prefix": "",
-    }
-    lang = config.lang.rscript
-    script = (
-        "file://../scripts/"
-        "scrna_metabolic_landscape/MetabolicPathwayActivity.R"
-    )
-    plugin_opts = {
-        "report": (
-            "file://../reports/"
-            "scrna_metabolic_landscape/MetabolicPathwayActivity.svelte"
-        )
-    }
-
-
-class MetabolicFeatures(Proc):
-    """Inter-subset metabolic features - Enrichment analysis in details
-
-    Requires:
-        - name: r-parallel
-        check: |
-            {{proc.lang}} <(echo "library(parallel)")
-        - name: r-fgsea
-        check: |
-            {{proc.lang}} <(echo "library(fgsea)")
-    """
-    input = "sobjfile:file"
-    output = "outdir:dir:{{in.sobjfile | stem}}.pathwayfeatures"
-    lang = config.lang.rscript
-    envs = {
-        "ncores": config.misc.ncores,
-        "fgsea": True,
-        "prerank_method": "signal_to_noise",
-        "top": 10,
-        "gmtfile": None,
-        "grouping": None,
-        "grouping_prefix": "",
-        "subsetting": None,
-        "subsetting_prefix": "",
-    }
-    script = "file://../scripts/scrna_metabolic_landscape/MetabolicFeatures.R"
-    plugin_opts = {
-        "report": (
-            "file://../reports/"
-            "scrna_metabolic_landscape/MetabolicFeatures.svelte"
-        )
-    }
-
-
-class MetabolicFeaturesIntraSubset(Proc):
-    """Intra-subset metabolic features - Enrichment analysis in details
-
-    Requires:
-        - name: r-parallel
-        check: |
-            {{proc.lang}} <(echo "library(parallel)")
-        - name: r-scater
-        check: |
-            {{proc.lang}} <(echo "library(scater)")
-        - name: r-fgsea
-        check: |
-            {{proc.lang}} <(echo "library(fgsea)")
-    """
-    input = "sobjfile:file"
-    output = "outdir:dir:{{in.sobjfile | stem}}.intra-subset-pathwayfeatures"
-    lang = config.lang.rscript
-    envs = {
-        "ncores": config.misc.ncores,
-        "gmtfile": None,
-        "fgsea": True,
-        "prerank_method": "signal_to_noise",
-        "top": 10,
-        "grouping": None,
-        "grouping_prefix": "",
-        "subsetting": None,
-        "subsetting_prefix": "",
-        "subsetting_comparison": {},
-    }
-    script = (
-        "file://../scripts/scrna_metabolic_landscape/"
-        "MetabolicFeaturesIntraSubsets.R"
-    )
-    plugin_opts = {
-        "report": (
-            "file://../reports/scrna_metabolic_landscape/"
-            "MetabolicFeaturesIntraSubsets.svelte"
-        )
-    }
-
-
-class MetabolicPathwayHeterogeneity(Proc):
-    """Pathway heterogeneity
-
-    Requires:
-        - name: r-gtools
-        check: |
-            {{proc.lang}} <(echo "library(gtools)")
-        - name: r-ggplot2
-        check: |
-            {{proc.lang}} <(echo "library(ggplot2)")
-        - name: r-ggprism
-        check: |
-            {{proc.lang}} <(echo "library(ggprism)")
-        - name: r-parallel
-        check: |
-            {{proc.lang}} <(echo "library(parallel)")
-        - name: r-dplyr
-        check: |
-            {{proc.lang}} <(echo "library(dplyr)")
-        - name: r-tibble
-        check: |
-            {{proc.lang}} <(echo "library(tibble)")
-        - name: r-enrichr
-        check: |
-            {{proc.lang}} <(echo "library(enrichR)")
-        - name: r-data.table
-        check: |
-            {{proc.lang}} <(echo "library(data.table)")
-        - name: r-fgsea
-        check: |
-            {{proc.lang}} <(echo "library(fgsea)")
-    """
-    input = "sobjfile:file"
-    output = "outdir:dir:{{in.sobjfile | stem}}.pathwayhetero"
-    lang = config.lang.rscript
-    envs = {
-        "gmtfile": None,
-        "select_pcs": 0.8,
-        "pathway_pval_cutoff": 0.01,
-        "ncores": config.misc.ncores,
-        "bubble_devpars": {},
-        "grouping": None,
-        "grouping_prefix": "",
-        "subsetting": None,
-        "subsetting_prefix": "",
-    }
-    script = (
-        "file://../scripts/scrna_metabolic_landscape/"
-        "MetabolicPathwayHeterogeneity.R"
-    )
-    plugin_opts = {
-        "report": (
-            "file://../reports/scrna_metabolic_landscape/"
-            "MetabolicPathwayHeterogeneity.svelte"
-        )
-    }
 
-
-class ScrnaMetabolicLandscape(Pipeline):
+class ScrnaMetabolicLandscape(ProcGroup):
     """Metabolic landscape analysis for scRNA-seq data
 
     An abstract from
@@ -224,72 +26,248 @@ class ScrnaMetabolicLandscape(Pipeline):
         "Metabolic landscape of the tumor microenvironment at
         single cell resolution." Nature communications 10.1 (2019): 1-12.
 
-    Input files:
-    - metafile: Either a metafile or an rds file of a Seurat object.
-        If it is a metafile, it should have two columns: `Sample` and
-        `RNADir`. `Sample` should be the first column with unique
-        identifiers for the samples and `RNADir` indicates where the
-        barcodes, genes, expression matrices are. The data will be loaded
-        and an unsupervised clustering will be done.
-        Currently only 10X data is supported.
-        If it is an rds file, the seurat object will be used directly
-    - is_seurat: Whether the input `metafile` is a seurat object.
-        If `metafile` is specified directly, this option will be ignored
-        and will be inferred from the file extension. If `metafile` is
-        not specified, meaning `<pipeline>.procs.MetabolicInput` is dependent
-        on other processes, this option will be used to determine whether
-        the input is a seurat object or not.
-    - gmtfile: The GMT file with the metabolic pathways. The gene names should
-        match the gene names in the gene list in RNADir or the Seurat object
-
-    Global options:
-    - grouping: defines the basic groups to investigate the metabolic activity
-        Typically the clusters.
-    - grouping_prefix: Working as a prefix to group names
-        For example, if we have `grouping_prefix = "cluster"` and
-        we have `1` and `2` in the `grouping` column, the groups
-        will be named as `cluster_1` and `cluster_2`
-    - subsetting: How do we subset the data. Another column in the metadata
-        to do comparisons.
-    - subsetting_prefix: Working as a prefix to subset names
-        For example, if we have `subsetting_prefix = "timepoint"` and
-        we have `pre` and `post` in the `subsetting` column, the subsets
-        will be named as `timepoint_pre` and `timepoint_post`
-    - subsetting_comparison: What kind of comparisons are we doing to compare
-        cells from different subsets.
-        It should be dict with keys as the names of the comparisons and
-        values as the 2 comparison groups from the `subsetting` column.
-        For example, if we have `pre` and `post` in the `subsetting` column,
-        we could have `subsetting_comparison = {"pre_vs_post": ["post", "pre"]}`
-        The second group will be the control group in the comparison.
-        If we also have `1`, `2` and `3` in the `grouping` column, by default,
-        the comparisons are done within each subset for each group. For example,
-        For group `1`, groups `2` and `3` will be used as control, and for
-        group `2`, groups `1` and `3` will be used as control, and for group
-        `3`, groups `1` and `2` will be used as control. It is similar to
-        `Seurat::FindMarkers` procedure. With this option, the comparisons
-        are also done to compare cells from different subsets within each group.
-        With the example above, we will have `pre_vs_post` comparisons within
-        each group.
-    - mutaters: Add new columns to the metadata for grouping/subsetting.
-        They are passed to `sobj@meta.data |> mutate(...)`. For example,
-        `{"timepoint": "if_else(treatment == 'control', 'pre', 'post')"}`
-        will add a new column `timepoint` to the metadata with values of
-        `pre` and `post` based on the `treatment` column.
-    - ncores: Number of cores to use for parallelization for each process
+    Args:
+        metafile: Either a metafile or an rds file of a Seurat object.
+            If it is a metafile, it should have two columns: `Sample` and
+            `RNADir`. `Sample` should be the first column with unique
+            identifiers for the samples and `RNADir` indicates where the
+            barcodes, genes, expression matrices are. The data will be loaded
+            and an unsupervised clustering will be done.
+            Currently only 10X data is supported.
+            If it is an rds file, the seurat object will be used directly
+        is_seurat: Whether the input `metafile` is a seurat object.
+            If `metafile` is specified directly, this option will be ignored
+            and will be inferred from the file extension. If `metafile` is
+            not specified, meaning `<pipeline>.procs.MetabolicInput` is
+            dependent on other processes, this option will be used to determine
+            whether the input is a seurat object or not.
+        gmtfile: The GMT file with the metabolic pathways. The gene names should
+            match the gene names in the gene list in RNADir or the Seurat object
+        grouping: defines the basic groups to investigate the metabolic activity
+            Typically the clusters.
+        grouping_prefix: Working as a prefix to group names
+            For example, if we have `grouping_prefix = "cluster"` and
+            we have `1` and `2` in the `grouping` column, the groups
+            will be named as `cluster_1` and `cluster_2`
+        subsetting: How do we subset the data. Another column in the metadata
+            to do comparisons.
+        subsetting_prefix: Working as a prefix to subset names
+            For example, if we have `subsetting_prefix = "timepoint"` and
+            we have `pre` and `post` in the `subsetting` column, the subsets
+            will be named as `timepoint_pre` and `timepoint_post`
+        subsetting_comparison: What kind of comparisons are we doing to compare
+            cells from different subsets.
+            It should be dict with keys as the names of the comparisons and
+            values as the 2 comparison groups from the `subsetting` column.
+            For example, if we have `pre` and `post` in the `subsetting` column,
+            we could have
+            `subsetting_comparison = {"pre_vs_post": ["post", "pre"]}`
+            The second group will be the control group in the comparison.
+            If we also have `1`, `2` and `3` in the `grouping` column,
+            by default, the comparisons are done within each subset for
+            each group. For example, for group `1`, groups `2` and `3`
+            will be used as control, and for group `2`, groups `1` and `3`
+            will be used as control, and for group `3`, groups `1` and `2`
+            will be used as control. It is similar to `Seurat::FindMarkers`
+            procedure. With this option, the comparisons are also done to
+            compare cells from different subsets within each group. With the
+            example above, we will have `pre_vs_post` comparisons within
+            each group.
+        mutaters: Add new columns to the metadata for grouping/subsetting.
+            They are passed to `sobj@meta.data |> mutate(...)`. For example,
+            `{"timepoint": "if_else(treatment == 'control', 'pre', 'post')"}`
+            will add a new column `timepoint` to the metadata with values of
+            `pre` and `post` based on the `treatment` column.
+        ncores: Number of cores to use for parallelization for each process
     """
+    DEFAULTS = Diot(
+        metafile=None,
+        is_seurat=None,
+        gmtfile=None,
+        grouping=None,
+        grouping_prefix="",
+        subsetting=None,
+        subsetting_prefix=None,
+        subsetting_comparison={},
+        mutaters=None,
+        ncores=config.misc.ncores,
+    )
 
-    defaults = config.pipeline.scrna_metabolic_landscape
+    class MetabolicPathwayActivity(Proc):
+        """Pathway activities for each group
+
+        Requires:
+            r-scater:
+                - check: {{proc.lang}} <(echo "library(scater)")
+            r-reshape2:
+                - check: {{proc.lang}} <(echo "library(reshape2)")
+            r-rcolorbrewer:
+                - check: {{proc.lang}} <(echo "library(RColorBrewer)")
+            r-ggplot2:
+                - check: {{proc.lang}} <(echo "library(ggplot2)")
+            r-ggprism:
+                - check: {{proc.lang}} <(echo "library(ggprism)")
+            r-complexheatmap:
+                - check: {{proc.lang}} <(echo "library(ComplexHeatmap)")
+            r-parallel:
+                - check: {{proc.lang}} <(echo "library(parallel)")
+        """
+        input = "sobjfile:file"
+        output = "outdir:dir:{{in.sobjfile | stem}}.pathwayactivity"
+        envs = {
+            "ntimes": 5000,
+            "ncores": config.misc.ncores,
+            "heatmap_devpars": {},
+            "violin_devpars": {},
+            "gmtfile": None,
+            "grouping": None,
+            "grouping_prefix": "",
+            "subsetting": None,
+            "subsetting_prefix": "",
+        }
+        lang = config.lang.rscript
+        script = (
+            "file://../scripts/"
+            "scrna_metabolic_landscape/MetabolicPathwayActivity.R"
+        )
+        plugin_opts = {
+            "report": (
+                "file://../reports/"
+                "scrna_metabolic_landscape/MetabolicPathwayActivity.svelte"
+            )
+        }
+
+    class MetabolicFeatures(Proc):
+        """Inter-subset metabolic features - Enrichment analysis in details
+
+        Requires:
+            r-parallel:
+                - check: {{proc.lang}} <(echo "library(parallel)")
+            r-fgsea:
+                - check: {{proc.lang}} <(echo "library(fgsea)")
+        """
+        input = "sobjfile:file"
+        output = "outdir:dir:{{in.sobjfile | stem}}.pathwayfeatures"
+        lang = config.lang.rscript
+        envs = {
+            "ncores": config.misc.ncores,
+            "fgsea": True,
+            "prerank_method": "signal_to_noise",
+            "top": 10,
+            "gmtfile": None,
+            "grouping": None,
+            "grouping_prefix": "",
+            "subsetting": None,
+            "subsetting_prefix": "",
+        }
+        script = (
+            "file://../scripts/scrna_metabolic_landscape/MetabolicFeatures.R"
+        )
+        plugin_opts = {
+            "report": (
+                "file://../reports/"
+                "scrna_metabolic_landscape/MetabolicFeatures.svelte"
+            )
+        }
+
+    class MetabolicFeaturesIntraSubset(Proc):
+        """Intra-subset metabolic features - Enrichment analysis in details
+
+        Requires:
+            r-parallel:
+                - check: {{proc.lang}} <(echo "library(parallel)")
+            r-scater:
+                - check: {{proc.lang}} <(echo "library(scater)")
+            r-fgsea:
+                - check: {{proc.lang}} <(echo "library(fgsea)")
+        """
+        input = "sobjfile:file"
+        output = (
+            "outdir:dir:{{in.sobjfile | stem}}.intra-subset-pathwayfeatures"
+        )
+        lang = config.lang.rscript
+        envs = {
+            "ncores": config.misc.ncores,
+            "gmtfile": None,
+            "fgsea": True,
+            "prerank_method": "signal_to_noise",
+            "top": 10,
+            "grouping": None,
+            "grouping_prefix": "",
+            "subsetting": None,
+            "subsetting_prefix": "",
+            "subsetting_comparison": {},
+        }
+        script = (
+            "file://../scripts/scrna_metabolic_landscape/"
+            "MetabolicFeaturesIntraSubsets.R"
+        )
+        plugin_opts = {
+            "report": (
+                "file://../reports/scrna_metabolic_landscape/"
+                "MetabolicFeaturesIntraSubsets.svelte"
+            )
+        }
+
+    class MetabolicPathwayHeterogeneity(Proc):
+        """Pathway heterogeneity
+
+        Requires:
+            r-gtools:
+                - check: {{proc.lang}} <(echo "library(gtools)")
+            r-ggplot2:
+                - check: {{proc.lang}} <(echo "library(ggplot2)")
+            r-ggprism:
+                - check: {{proc.lang}} <(echo "library(ggprism)")
+            r-parallel:
+                - check: {{proc.lang}} <(echo "library(parallel)")
+            r-dplyr:
+                - check: {{proc.lang}} <(echo "library(dplyr)")
+            r-tibble:
+                - check: {{proc.lang}} <(echo "library(tibble)")
+            r-enrichr:
+                - check: {{proc.lang}} <(echo "library(enrichR)")
+            r-data.table:
+                - check: {{proc.lang}} <(echo "library(data.table)")
+            r-fgsea:
+                - check: {{proc.lang}} <(echo "library(fgsea)")
+        """
+        input = "sobjfile:file"
+        output = "outdir:dir:{{in.sobjfile | stem}}.pathwayhetero"
+        lang = config.lang.rscript
+        envs = {
+            "gmtfile": None,
+            "select_pcs": 0.8,
+            "pathway_pval_cutoff": 0.01,
+            "ncores": config.misc.ncores,
+            "bubble_devpars": {},
+            "grouping": None,
+            "grouping_prefix": "",
+            "subsetting": None,
+            "subsetting_prefix": "",
+        }
+        script = (
+            "file://../scripts/scrna_metabolic_landscape/"
+            "MetabolicPathwayHeterogeneity.R"
+        )
+        plugin_opts = {
+            "report": (
+                "file://../reports/scrna_metabolic_landscape/"
+                "MetabolicPathwayHeterogeneity.svelte"
+            )
+        }
+
+    def post_init(self):
+        """Load runtime processes"""
+        if self.opts.metafile:
+            suffix = Path(self.opts.metafile).suffix
+            self.opts.is_seurat = suffix in (".rds", ".RDS")
 
-    @process(start=True)
-    def build_input(self) -> Type[Proc]:
+    @ProcGroup.add_proc
+    def p_input(self) -> Type[Proc]:
         """Build MetabolicInputs process"""
         from .misc import File2Proc
 
-        if self.options.metafile:
-            suffix = Path(self.options.metafile).suffix
-            self.options.is_seurat = suffix in (".rds", ".RDS")
-
         class MetabolicInput(File2Proc):
             """Input for the metabolic pathway analysis pipeline for
             scRNA-seq data
@@ -302,159 +280,139 @@ class ScrnaMetabolicLandscape(Pipeline):
                 metafile: Soft link to `in.metafile`
             """
 
-            if self.options.metafile:
-                input_data = [self.options.metafile]
+            if self.opts.metafile:
+                input_data = [self.opts.metafile]
 
         return MetabolicInput
 
-    @process
-    def build_preparing(self, input_proc: Type[Proc]) -> Type[Proc]:
+    @ProcGroup.add_proc
+    def p_preparing(self) -> Type[Proc]:
         """Build SeuratPreparing process"""
         from .scrna import SeuratPreparing
 
         class SeuratPreparing(SeuratPreparing):
-            requires = input_proc
+            requires = self.p_input
 
         return SeuratPreparing
 
-    @process
-    def build_clustering(self, preparing_proc: Type[Proc]) -> Type[Proc]:
+    @ProcGroup.add_proc
+    def p_clustering(self) -> Type[Proc]:
         """Build SeuratClustering process"""
+        if self.opts.is_seurat:
+            return self.p_input
+
         from .scrna import SeuratClustering
 
         class SeuratClustering(SeuratClustering):
-            requires = preparing_proc
+            requires = self.p_preparing
 
         return SeuratClustering
 
-    @process
-    def build_mutater(self, clustering_proc: Type[Proc]) -> Type[Proc]:
+    @ProcGroup.add_proc
+    def p_mutater(self) -> Type[Proc]:
         """Build SeuratMetadataMutater process"""
+        if self.opts.mutaters:
+            return self.p_clustering
+
         from .scrna import SeuratMetadataMutater
 
         class SeuratMetadataMutater(SeuratMetadataMutater):
-            requires = clustering_proc
+            requires = self.p_clustering
             input_data = lambda ch: tibble(
                 srtobj=ch.iloc[:, 0],
                 metafile=[None],
-                mutaters=[self.options.mutaters],
+                mutaters=[self.opts.mutaters],
             )
 
         return SeuratMetadataMutater
 
-    @process
-    def build_expr_impute(self, subset_proc: Type[Proc]) -> Type[Proc]:
+    @ProcGroup.add_proc
+    def p_expr_impute(self) -> Type[Proc]:
         """Build MetabolicExprImpute process"""
         from .scrna import ExprImpute
 
         class MetabolicExprImpute(ExprImpute):
-            requires = subset_proc
+            requires = self.p_mutater
 
         return MetabolicExprImpute
 
-    @process(end=True)
-    def build_pathway_activity(self, expr_imp_proc: Type[Proc]) -> Type[Proc]:
+    @ProcGroup.add_proc
+    def p_pathway_activity(self) -> Type[Proc]:
         """Build MetabolicPathwayActivity process"""
         return Proc.from_proc(
-            MetabolicPathwayActivity,
+            ScrnaMetabolicLandscape.MetabolicPathwayActivity,
             "MetabolicPathwayActivity",
-            requires=expr_imp_proc,
+            requires=self.p_expr_impute,
             order=-1,
             envs={
-                "ncores": self.options.ncores,
-                "gmtfile": self.options.gmtfile,
-                "grouping": self.options.grouping,
-                "grouping_prefix": self.options.grouping_prefix,
-                "subsetting": self.options.subsetting,
-                "subsetting_prefix": self.options.subsetting_prefix,
+                "ncores": self.opts.ncores,
+                "gmtfile": self.opts.gmtfile,
+                "grouping": self.opts.grouping,
+                "grouping_prefix": self.opts.grouping_prefix,
+                "subsetting": self.opts.subsetting,
+                "subsetting_prefix": self.opts.subsetting_prefix,
             },
         )
 
-    @process(end=True)
-    def build_pathway_heterogeneity(self, norm_proc: Type[Proc]) -> Type[Proc]:
+    @ProcGroup.add_proc
+    def p_pathway_heterogeneity(self) -> Type[Proc]:
         """Build MetabolicPathwayHeterogeneity process"""
         return Proc.from_proc(
-            MetabolicPathwayHeterogeneity,
+            ScrnaMetabolicLandscape.MetabolicPathwayHeterogeneity,
             "MetabolicPathwayHeterogeneity",
-            requires=norm_proc,
+            requires=self.p_expr_impute,
             envs={
-                "ncores": self.options.ncores,
-                "gmtfile": self.options.gmtfile,
-                "grouping": self.options.grouping,
-                "grouping_prefix": self.options.grouping_prefix,
-                "subsetting": self.options.subsetting,
-                "subsetting_prefix": self.options.subsetting_prefix,
+                "ncores": self.opts.ncores,
+                "gmtfile": self.opts.gmtfile,
+                "grouping": self.opts.grouping,
+                "grouping_prefix": self.opts.grouping_prefix,
+                "subsetting": self.opts.subsetting,
+                "subsetting_prefix": self.opts.subsetting_prefix,
             },
         )
 
-    @process(end=True)
-    def build_features(self, norm_proc: Type[Proc]) -> Type[Proc]:
+    @ProcGroup.add_proc
+    def p_features(self) -> Type[Proc]:
         """Build MetabolicFeatures process"""
         return Proc.from_proc(
-            MetabolicFeatures,
+            ScrnaMetabolicLandscape.MetabolicFeatures,
             "MetabolicFeatures",
-            requires=norm_proc,
+            requires=self.p_expr_impute,
             envs={
-                "ncores": self.options.ncores,
-                "gmtfile": self.options.gmtfile,
-                "grouping": self.options.grouping,
-                "grouping_prefix": self.options.grouping_prefix,
-                "subsetting": self.options.subsetting,
-                "subsetting_prefix": self.options.subsetting_prefix,
+                "ncores": self.opts.ncores,
+                "gmtfile": self.opts.gmtfile,
+                "grouping": self.opts.grouping,
+                "grouping_prefix": self.opts.grouping_prefix,
+                "subsetting": self.opts.subsetting,
+                "subsetting_prefix": self.opts.subsetting_prefix,
             },
         )
 
-    @process(end=True)
-    def build_features_intra_subset(self, norm_proc: Type[Proc]) -> Type[Proc]:
+    @ProcGroup.add_proc
+    def p_features_intra_subset(self) -> Type[Proc]:
         """Build MetabolicFeaturesIntraSubset process"""
-        if self.options.subsetting_comparison and not self.options.subsetting:
+        if self.opts.subsetting_comparison and not self.opts.subsetting:
             raise ValueError(
                 "Cannot use `subsetting_comparison` without `subsetting`."
             )
 
         return Proc.from_proc(
-            MetabolicFeaturesIntraSubset,
+            ScrnaMetabolicLandscape.MetabolicFeaturesIntraSubset,
             "MetabolicFeaturesIntraSubset",
-            requires=norm_proc,
+            requires=self.p_expr_impute,
             envs={
-                "ncores": self.options.ncores,
-                "gmtfile": self.options.gmtfile,
-                "grouping": self.options.grouping,
-                "grouping_prefix": self.options.grouping_prefix,
-                "subsetting": self.options.subsetting,
-                "subsetting_prefix": self.options.subsetting_prefix,
-                "subsetting_comparison": self.options.subsetting_comparison,
+                "ncores": self.opts.ncores,
+                "gmtfile": self.opts.gmtfile,
+                "grouping": self.opts.grouping,
+                "grouping_prefix": self.opts.grouping_prefix,
+                "subsetting": self.opts.subsetting,
+                "subsetting_prefix": self.opts.subsetting_prefix,
+                "subsetting_comparison": self.opts.subsetting_comparison,
             },
         )
 
-    def build(self) -> None:
-        """Build processes for metabolic landscape analysis pipeline"""
-        self.options = DEFAULT_OPTS | self.options
-
-        if not self.options.gmtfile:
-            raise ValueError("`gmtfile` with metabolic pathways is required.")
-
-        MetabolicInput = self.build_input()
-
-        if self.options.is_seurat:
-            # Use the rds file
-            SeuratClustering = MetabolicInput
-        else:
-            # Do clustering
-            SeuratPreparing = self.build_preparing(MetabolicInput)
-            SeuratClustering = self.build_clustering(SeuratPreparing)
-
-        if self.options.mutaters:
-            SeuratMetadataMutater = self.build_mutater(SeuratClustering)
-        else:
-            # No mutaters, just use the SeuratClustering
-            SeuratMetadataMutater = SeuratClustering
-
-        # Do imputation and normalization for all the data together
-        MetabolicExprImpute = self.build_expr_impute(SeuratMetadataMutater)
-
-        self.build_pathway_activity(MetabolicExprImpute)
-        self.build_pathway_heterogeneity(MetabolicExprImpute)
-        self.build_features(MetabolicExprImpute)
-        if self.options.subsetting_comparison:
-            self.build_features_intra_subset(MetabolicExprImpute)
+
+if __name__ == "__main__":
+    from pipen_args import install  # noqa: F401
+
+    ScrnaMetabolicLandscape().as_pipen().run()