biopipen 0.21.2__py3-none-any.whl → 0.22.1__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.21.2"
+__version__ = "0.22.1"

biopipen/core/filters.py

@@ -7,6 +7,7 @@ from typing import Any, List, Mapping
 
 from argx import Namespace
 from liquid.filters.manager import FilterManager
+from pipen_report.filters import register_component, render_ui, _tag
 
 filtermanager = FilterManager()
 
@@ -206,3 +207,144 @@ def r(
         return r(vars(obj), ignoreintkey, todot, sortkeys, skip, _i)
 
     return repr(obj)
+
+
+@register_component("fgsea")
+def _render_fgsea(
+    cont: Mapping[str, Any],
+    job: Mapping[str, Any],
+    level: int,
+    na_arg: str = "10",
+) -> str:
+    """Render fgsea report"""
+    # cont["dir"] is required
+    n_pathways = int(na_arg)
+    pathways = []
+    with Path(cont["dir"]).joinpath("fgsea.txt").open() as f:
+        next(f)  # skip header
+        for line in f:
+            pathway, _ = line.split("\t", 1)
+            pathways.append(pathway)
+            if len(pathways) >= n_pathways:
+                break
+
+    components = [
+        # Summary
+        {
+            "title": "Enrichment Analysis Summary",
+            "ui": "tabs",
+            "contents": [
+                {
+                    "title": "Plot",
+                    "ui": "flat",
+                    "contents": [
+                        {
+                            "kind": "image",
+                            "src": str(Path(cont["dir"]).joinpath("gsea_table.png")),
+                        }
+                    ],
+                },
+                {
+                    "title": "Table",
+                    "ui": "flat",
+                    "contents": [
+                        {
+                            "kind": "table",
+                            "src": str(Path(cont["dir"]).joinpath("fgsea.txt")),
+                        }
+                    ],
+                },
+            ]
+        },
+        # Pathways
+        {
+            "title": f"Enriched Pathways (Top {n_pathways})",
+            "ui": "table_of_images",
+            "contents": [
+                {
+                    "src": str(Path(cont["dir"]) / f"fgsea_{pw.replace('/', '-')}.png"),
+                    "title": pw,
+                }
+                for pw in pathways
+            ]
+        },
+    ]
+
+    return render_ui(components, "accordion", job, level)
+
+
+@register_component("pdf")
+def _render_pdf(
+    cont: Mapping[str, Any],
+    job: Mapping[str, Any],
+    level: int,
+) -> str:
+    """Render pdf report"""
+    # cont["src"] is required
+    height = cont.get("height", "600")
+    return _tag(
+        "embed",
+        src=str(cont["src"]),
+        type="application/pdf",
+        width="100%",
+        height=height,
+    )
+
+
+@register_component("gsea")
+def _render_gsea(
+    cont: Mapping[str, Any],
+    job: Mapping[str, Any],
+    level: int,
+) -> str:
+    """Render gsea report"""
+    # cont["dir"] is required
+    raise NotImplementedError()
+
+
+@register_component("enrichr")
+def _render_enrichr(
+    cont: Mapping[str, Any],
+    job: Mapping[str, Any],
+    level: int,
+) -> str:
+    """Render enrichr report"""
+    # cont["dir"] is required
+    dbs = [sumfile.stem[8:] for sumfile in Path(cont["dir"]).glob("Enrichr-*.txt")]
+    components = []
+
+    for db in dbs:
+        components.append(
+            {
+                "title": db,
+                "ui": "tabs",
+                "contents": [
+                    {
+                        "title": "Plot",
+                        "ui": "flat",
+                        "contents": [
+                            {
+                                "kind": "image",
+                                "src": str(
+                                    Path(cont["dir"]).joinpath(f"Enrichr-{db}.png")
+                                ),
+                            }
+                        ],
+                    },
+                    {
+                        "title": "Table",
+                        "ui": "flat",
+                        "contents": [
+                            {
+                                "kind": "table",
+                                "src": str(
+                                    Path(cont["dir"]).joinpath(f"Enrichr-{db}.txt")
+                                ),
+                            }
+                        ],
+                    },
+                ],
+            }
+        )
+
+    return render_ui(components, "accordion", job, level)

biopipen/ns/scrna.py

@@ -257,6 +257,16 @@ class SeuratClustering(Proc):
             `object` is specified internally, and `-` in the key will be replaced with `.`.
             - resolution (type=float): The resolution of the clustering
             - <more>: See <https://satijalab.org/seurat/reference/findclusters>
+        cache (type=auto): Whether to cache the seurat object with cluster information.
+            If `True`, the seurat object will be cached in the job output directory, which will be not cleaned up when job is rerunning.
+            The cached seurat object will be saved as `<signature>.cached.RDS` file, where `<signature>` is the signature determined by
+            the input and envs of the process.
+            See <https://github.com/satijalab/seurat/issues/7849>, <https://github.com/satijalab/seurat/issues/5358> and
+            <https://github.com/satijalab/seurat/issues/6748> for more details.
+            To not use the cached seurat object, you can either set `cache` to `False` or delete the cached file at
+            `.pipen/<Pipeline>/SeuratClustering/0/output/<signature>.cached.RDS`.
+            You can also specify the directory to save the cached seurat object by setting `cache` to the directory path.
+
 
     Requires:
         r-seurat:
@@ -286,6 +296,7 @@ class SeuratClustering(Proc):
         "RunUMAP": {"reduction": "pca", "dims": 30},
         "FindNeighbors": {},
         "FindClusters": {"resolution": 0.8},
+        "cache": True,
     }
     script = "file://../scripts/scrna/SeuratClustering.R"
 
@@ -418,6 +429,7 @@ class SeuratClusterStats(Proc):
             - group-by: Same as `ident`. How the points are colored.
             - split-by: The column name in metadata to split the cells into different plots.
             - shape-by: The column name in metadata to use as the shape.
+            - subset: An expression to subset the cells, will be passed to `tidyrseurat::filter()`.
             - devpars (ns): The device parameters for the plots.
                 - res (type=int): The resolution of the plots.
                 - height (type=int): The height of the plots.
@@ -482,6 +494,7 @@ class SeuratClusterStats(Proc):
             "group-by": None,
             "split-by": None,
             "shape-by": None,
+            "subset": None,
             "reduction": "dim",
             "devpars": {"res": 100, "height": 800, "width": 1000},
         },
@@ -642,6 +655,7 @@ class CellsDistribution(Proc):
             Ignored if `cells_order` is specified.
         subset: An expression to subset the cells, will be passed to `dplyr::filter()` on metadata.
             This will be applied prior to `each`.
+        descr: The description of the case, will be shown in the report.
         devpars (ns): The device parameters for the plots.
             - res (type=int): The resolution of the plots
             - height (type=int): The height of the plots
@@ -676,6 +690,7 @@ class CellsDistribution(Proc):
         "cells_orderby": None,
         "cells_n": 10,
         "subset": None,
+        "descr": None,
         "devpars": {},
         "each": None,
         "section": "DEFAULT",
@@ -1669,7 +1684,7 @@ class RadarPlots(Proc):
         "cluster_order": [],
         "breaks": [],
         "direction": "intra-cluster",
-        "section": None,
+        "section": "DEFAULT",
         "devpars": {
             "res": 100,
             "width": 1200,
@@ -1719,6 +1734,8 @@ class MetaMarkers(Proc):
         dbs (list): The dbs to do enrichment analysis for significant
             markers See below for all libraries.
             <https://maayanlab.cloud/Enrichr/#libraries>
+        subset: The subset of the cells to do the analysis.
+            An expression passed to `dplyr::filter()`.
         p_adjust (choice): The method to adjust the p values, which can be used to filter the significant markers.
             See also <https://rdrr.io/r/stats/p.adjust.html>
             - holm: Holm-Bonferroni method
@@ -1759,6 +1776,7 @@ class MetaMarkers(Proc):
         "group-by": None,
         "idents": None,
         "each": None,
+        "subset": None,
         "prefix_each": True,
         "p_adjust": "BH",
         "dbs": [

biopipen/ns/tcr.py

@@ -40,11 +40,13 @@ class ImmunarchLoading(Proc):
 
     Output:
         rdsfile: The RDS file with the data and metadata
-        metatxt: The meta data of the cells, used to attach to the Seurat object
+        metatxt: The meta data at cell level, which can be used to attach to the Seurat object
 
     Envs:
         prefix: The prefix to the barcodes. You can use placeholder like `{Sample}_`
-            to use the meta data from the `immunarch` object.
+            to use the meta data from the `immunarch` object. The prefixed barcodes will
+            be saved in `out.metatxt`. The `immunarch` object keeps the original barcodes, but
+            the prefix is saved at `immdata$prefix`.
 
             /// Note
             This option is useful because the barcodes for the cells from scRNA-seq
@@ -65,10 +67,16 @@ class ImmunarchLoading(Proc):
             paired chain data. For `single`, only TRB chain will be kept
             at `immdata$data`, information for other chains will be
             saved at `immdata$tra` and `immdata$multi`.
-        metacols (list): The columns to be exported to the text file.
+        extracols (list): The extra columns to be exported to the text file.
             You can refer to the
             [immunarch documentation](https://immunarch.com/articles/v2_data.html#immunarch-data-format)
-            for the full list of the columns.
+            to get a sense for the full list of the columns.
+            The columns may vary depending on the data source.
+            The columns from `immdata$meta` and some core columns, including
+            `Barcode`, `CDR3.aa`, `Clones`, `Proportion`, `V.name`, `J.name`, and
+            `D.name` will be exported by default. You can use this option to
+            specify the extra columns to be exported.
+
     """  # noqa: E501
     input = "metafile:file"
     output = [
@@ -80,7 +88,7 @@ class ImmunarchLoading(Proc):
         "tmpdir": config.path.tmpdir,
         "prefix": "{Sample}_",
         "mode": "single",
-        "metacols": ["Clones", "Proportion", "CDR3.aa"],
+        "extracols": [],
     }
     script = "file://../scripts/tcr/ImmunarchLoading.R"
 
@@ -322,6 +330,7 @@ class Immunarch(Proc):
         prefix: The prefix to the barcodes. You can use placeholder like `{Sample}_`
             The prefixed barcodes will be used to match the barcodes in `in.metafile`.
             Not used if `in.metafile` is not specified.
+            If `None` (default), `immdata$prefix` will be used.
         volumes (ns): Explore clonotype volume (sizes).
             - by: Groupings when visualize clonotype volumes, passed to the `.by` argument of `vis(imm_vol, .by = <values>)`.
                 Multiple columns should be separated by `,`.
@@ -682,7 +691,7 @@ class Immunarch(Proc):
     lang = config.lang.rscript
     envs = {
         "mutaters": {},
-        "prefix": "{Sample}_",
+        "prefix": None,
         # basic statistics
         "volumes": {
             "by": None,
@@ -1179,6 +1188,10 @@ class TCRClustering(Proc):
             For GIANA, using TRBV mutations is not supported
             - GIANA: by Li lab at UT Southwestern Medical Center
             - ClusTCR: by Sebastiaan Valkiers, etc
+        prefix: The prefix to the barcodes. You can use placeholder like `{Sample}_`
+            The prefixed barcodes will be used to match the barcodes in `in.metafile`.
+            Not used if `in.metafile` is not specified.
+            If `None` (default), `immdata$prefix` will be used.
         python: The path of python with `GIANA`'s dependencies installed
             or with `clusTCR` installed. Depending on the `tool` you choose.
         args (type=json): The arguments for the clustering tool
@@ -1202,6 +1215,7 @@ class TCRClustering(Proc):
     lang = config.lang.rscript
     envs = {
         "tool": "GIANA",  # or ClusTCR
+        "prefix": None,
         "on_multi": False,
         "python": config.lang.python,
         "args": {},
@@ -1507,7 +1521,8 @@ class TESSA(Proc):
             [link](https://www.nature.com/articles/s42256-021-00383-2)
 
     Input:
-        immdata: The data loaded by `immunarch::repLoad()`, saved in RDS format
+        immdata: The immunarch object in RDS file or text file of TCR data loaded by
+            [`ImmunarchLoading`](!!#biopipennstcrimmunarchloading)
         srtobj: The `Seurat` object, saved in RDS format, with dimension
             reduction performed if you want to use them to represent the
             transcriptome of T cells.
@@ -1522,8 +1537,13 @@ class TESSA(Proc):
 
     Envs:
         python: The path of python with `TESSA`'s dependencies installed
-        prefix: The prefix to the barcodes of TCR data. You can use placeholder
-            like `{Sample}_` to use the meta data from the immunarch object.
+        prefix: The prefix of the cell barcodes in the `Seurat` object.
+            Once could use a fixed prefix, or a placeholder with the column
+            name in meta data. For example, `"{Sample}_"` will replace the
+            placeholder with the value of the column `Sample` in meta data.
+            If `in.immdata` is text file, the prefix will be ignored and the
+            barcode should be already prefixed.
+            If `None` and `in.immdata` is RDS file, `immdata$prefix` will be used.
         within_sample (flag): Whether the TCR networks are constructed only
             within TCRs from the same sample/patient (True) or with all the
             TCRs in the meta data matrix (False).
@@ -1548,7 +1568,7 @@ class TESSA(Proc):
     lang = config.lang.rscript
     envs = {
         "python": config.lang.python,
-        "prefix": "{Sample}_",
+        "prefix": None,
         "assay": "RNA",
         "within_sample": False,
         "predefined_b": False,

biopipen/reports/delim/SampleInfo.svelte

@@ -1,31 +1,11 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 
 <script>
-    import { Image, DataTable } from "$libs";
+    import { Image, DataTable, Descr } from "$libs";
 </script>
 
 {%- macro report_job(job, h=1) -%}
-
-    {% if envs.stats %}
-    <h{{h}}>Sample Information</h{{h}}>
-    {% endif %}
-    {% if envs.exclude_cols and isinstance(envs.exclude_cols, str) %}
-        {% set excluded_cols = envs.exclude_cols | replace: " ", "" | split: "," %}
-    {% else %}
-        {% set excluded_cols = envs.exclude_cols %}
-    {% endif %}
-
-    <DataTable
-        data={ {{ job.out.outfile | datatable: sep="\t", excluded=excluded_cols }} }
-        pageSize={50}
-        />
-
-    {% if envs.stats %}
-        <h{{h}}>Statistics</h{{h}}>
-        {%- set stat_imgs = job.outdir | glob: "*.png" -%}
-        {{- table_of_images(stat_imgs) -}}
-    {% endif %}
-
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}

biopipen/reports/scrna/CellsDistribution.svelte

@@ -1,50 +1,15 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 <script>
-    import { Image } from "$libs";
+    import { Image, DataTable, Descr } from "$libs";
+    import { Tabs, Tab, TabContent } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=1) -%}
-    {%- set secdirs = job.out.outdir | glob: "*" -%}
-    {%- if len(secdirs) == 1 -%}
-        {%- set secname = secdirs | first | basename -%}
-        {%- if secdirs[0] | joinpaths: "venn.png" | exists -%}
-            {%- if secname == "DEFAULT" -%}
-                <h{{h}}>Case overlapping</h{{h}}>
-            {%- else -%}
-                <h{{h}}>{{ secname | escape }} - Case overlapping</h{{h}}>
-            {%- endif -%}
-            {{ table_of_images(
-                [joinpaths(secdirs[0], "venn.png"), joinpaths(secdirs[0], "upset.png")],
-                ["Venn plot", "Upset plot"]) }}
-        {%- endif -%}
-        {%- for plotfile in secdirs[0] | glob: "case-*.png" -%}
-            {%- if secname == "DEFAULT" -%}
-                <h{{h}}>{{ plotfile | stem | escape }}</h{{h}}>
-            {%- else -%}
-                <h{{h}}>{{ secname | escape }} - {{ plotfile | stem | escape }}</h{{h}}>
-            {%- endif -%}
-            <Image src={{plotfile | quote}} />
-        {%- endfor -%}
-    {%- else -%}
-        {%- for secdir in secdirs -%}
-            {%- set sec = secdir | basename -%}
-            <h{{h}}>{{sec | escape}}</h{{h}}>
-            {%- if secdir | joinpaths: "venn.png" | exists -%}
-                <h{{h+1}}>Case overlapping</h{{h+1}}>
-                {{ table_of_images(
-                    [joinpaths(secdir, "venn.png"), joinpaths(secdir, "upset.png")],
-                    ["Venn plot", "Upset plot"]) }}
-            {%- endif -%}
-            {%- for plotfile in secdir | glob: "case-*.png" -%}
-                <h{{h+1}}>{{ plotfile | stem }}</h{{h+1}}>
-                <Image src={{plotfile | quote}} />
-            {%- endfor -%}
-        {%- endfor -%}
-    {%- endif -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}
-<h1>{{job.in.srtobj | stem0 | escape}}</h1>
+    <h1>{{job.in.srtobj | stem0 | escape}}</h1>
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna/MarkersFinder.svelte

@@ -1,138 +1,18 @@
 {% from "utils/misc.liq" import report_jobs -%}
-{% from "utils/gsea.liq" import enrichr_report -%}
+
 <script>
-    import { Image, DataTable } from "$libs";
-    import { Tabs, Tab, TabContent, InlineNotification } from "$ccs";
+    import { Image, DataTable, Descr } from "$libs";
+    import { Tabs, Tab, TabContent, InlineNotification, Accordion, AccordionItem } from "$ccs";
 </script>
 
 
 {%- macro report_job(job, h=1) -%}
-    {%- set alldirs = job.out.outdir | glob: "*" -%}
-    {%- set ovdir = job.out.outdir | joinpaths: "OVERLAPS" -%}
-    {%- set secdirs = [] -%}
-    {%- for adir in alldirs -%}
-        {%- if basename(adir) != "OVERLAPS" -%}
-            {%- set _ = secdirs.append(adir) -%}
-        {%- endif -%}
-    {%- endfor -%}
-
-    {%- if len(secdirs) == 1 -%}
-        {%- set secname = secdirs | first | basename -%}
-        {%- for casedir in secdirs[0] | glob: "*" -%}
-            {%- if secname == "DEFAULT" -%}
-                <h{{h}}>{{casedir | basename | escape}}</h{{h}}>
-            {%- else -%}
-                <h{{h}}>{{secname | escape}} - {{casedir | basename | escape}}</h{{h}}>
-            {%- endif -%}
-            {%- if casedir | joinpaths: "error.txt" | exists -%}
-                <InlineNotification
-                    hideCloseButton
-                    lowContrast
-                    kind="warning"
-                    subtitle={{ casedir | joinpaths: "error.txt" | read | quote }}
-                    />
-            {%- else -%}
-                <h{{h+1}}>Markers</h{{h+1}}>
-                <Tabs>
-                    <Tab label="Markers" />
-                    <Tab label="Volcano Plot" />
-                    <Tab label="Dot Plot" />
-                    <svelte:fragment slot="content">
-                        <TabContent>
-                            <DataTable
-                                src={{ casedir | joinpaths: "markers.txt" | quote }}
-                                data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t", nrows=100 }} }
-                                />
-                        </TabContent>
-                        <TabContent>
-                            <Image src={{ casedir | joinpaths: "volcano.png" | quote }} />
-                        </TabContent>
-                        <TabContent>
-                            <Image src={{ casedir | joinpaths: "dotplot.png" | quote }} />
-                        </TabContent>
-                    </svelte:fragment>
-                </Tabs>
-
-                <h{{h+1}}>Enrichment analysis</h{{h+1}}>
-                {{ enrichr_report(casedir) }}
-            {%- endif -%}
-        {%- endfor -%}
-    {%- else -%}
-        {%- for secdir in secdirs -%}
-            {%- set sec = secdir | basename -%}
-            <h{{h}}>{{sec | escape}}</h{{h}}>
-            {%- for casedir in secdir | glob: "*" -%}
-                <h{{h+1}}>{{casedir | basename | escape}}</h{{h+1}}>
-                {%- if casedir | joinpaths: "error.txt" | exists -%}
-                    <InlineNotification
-                        hideCloseButton
-                        lowContrast
-                        kind="warning"
-                        subtitle={{ casedir | joinpaths: "error.txt" | read | quote }}
-                        />
-                {%- else -%}
-                    <h{{h+2}}>Markers</h{{h+2}}>
-                    <Tabs>
-                        <Tab label="Markers" />
-                        <Tab label="Volcano Plot" />
-                        <Tab label="Dot Plot" />
-                        <svelte:fragment slot="content">
-                            <TabContent>
-                                <DataTable
-                                    src={{ casedir | joinpaths: "markers.txt" | quote }}
-                                    data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t", nrows=100 }} }
-                                    />
-                            </TabContent>
-                            <TabContent>
-                                <Image src={{ casedir | joinpaths: "volcano.png" | quote }} />
-                            </TabContent>
-                            <TabContent>
-                                <Image src={{ casedir | joinpaths: "dotplot.png" | quote }} />
-                            </TabContent>
-                        </svelte:fragment>
-                    </Tabs>
-
-                    <h{{h+2}}>Enrichment analysis</h{{h+2}}>
-                    {{ enrichr_report(casedir) }}
-                {%- endif -%}
-            {%- endfor -%}
-        {%- endfor -%}
-    {%- endif -%}
-
-    {%- if ovdir | exists -%}
-        <h{{h}}>Overlapping Markers</h{{h}}>
-        {%- for casedir in ovdir | glob: "*" -%}
-            <h{{h+1}}>{{casedir | basename | escape}}</h{{h+1}}>
-            <Tabs>
-                {%- if casedir | joinpaths: "venn.png" | exists -%}
-                <Tab label="Venn Diagram" />
-                {%- endif -%}
-                <Tab label="UpSet Plot" />
-                <Tab label="Marks" />
-                <svelte:fragment slot="content">
-                    {%- if casedir | joinpaths: "venn.png" | exists -%}
-                    <TabContent>
-                        <Image src={{ casedir | joinpaths: "venn.png" | quote }} />
-                    </TabContent>
-                    {%- endif -%}
-                    <TabContent>
-                        <Image src={{ casedir | joinpaths: "upset.png" | quote }} />
-                    </TabContent>
-                    <TabContent>
-                        <DataTable
-                            src={{ casedir | joinpaths: "markers.txt" | quote }}
-                            data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t" }} }
-                            />
-                    </TabContent>
-                </svelte:fragment>
-            </Tabs>
-        {%- endfor -%}
-    {%- endif -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 
 {%- macro head_job(job) -%}
-  <h1>{{job.in.srtobj | stem | escape}}</h1>
+    <h1>{{job.in.srtobj | stem | escape}}</h1>
 {%- endmacro -%}
 
-{{ report_jobs(jobs, head_job, report_job) }}
+{{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna/MetaMarkers.svelte

@@ -1,85 +1,13 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 {% from "utils/gsea.liq" import enrichr_report -%}
 <script>
-    import { Image, DataTable } from "$libs";
-    import { Tabs, Tab, TabContent, InlineNotification } from "$ccs";
+    import { Image, DataTable, Descr } from "$libs";
+    import { Tabs, Tab, TabContent, InlineNotification, Accordion, AccordionItem } from "$ccs";
 </script>
 
 
 {%- macro report_job(job, h=1) -%}
-    {%- set secdirs = job.out.outdir | glob: "*" -%}
-    {%- if len(secdirs) == 1 -%}
-        {%- set secname = secdirs | first | basename -%}
-        {%- for casedir in secdirs[0] | glob: "*" -%}
-            {%- if secname == "DEFAULT" -%}
-                <h{{h}}>{{casedir | basename | escape}}</h{{h}}>
-            {%- else -%}
-                <h{{h}}>{{secname | escape}} - {{casedir | basename | escape}}</h{{h}}>
-            {%- endif -%}
-            {%- if casedir | joinpaths: "error.txt" | exists -%}
-                <InlineNotification
-                    hideCloseButton
-                    lowContrast
-                    kind="warning"
-                    subtitle={{ casedir | joinpaths: "error.txt" | read | quote }}
-                    />
-            {%- else -%}
-                <h{{h+1}}>Markers</h{{h+1}}>
-                <Tabs>
-                    <Tab label="Top 10 genes" />
-                    <Tab label="Table of top 100 genes" />
-                    <div slot="content">
-                    <TabContent>
-                        {{ table_of_images(glob(casedir, "plots", "*.png"), col = 4) }}
-                    </TabContent>
-                    <TabContent>
-                        <DataTable
-                            src={{ casedir | joinpaths: "markers.txt" | quote }}
-                            data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t", nrows=100 }} }
-                            />
-                    </TabContent>
-                    </div>
-                </Tabs>
-
-                <h{{h+1}}>Enrichment analysis</h{{h+1}}>
-                {{ enrichr_report(casedir) }}
-            {%- endif -%}
-        {%- endfor -%}
-    {%- else -%}
-        {%- for secdir in secdirs -%}
-            {%- set sec = secdir | basename -%}
-            <h{{h}}>{{sec | escape}}</h{{h}}>
-            {%- for casedir in secdir | glob: "*" -%}
-                <h{{h+1}}>{{casedir | basename | escape}}</h{{h+1}}>
-                {%- if casedir | joinpaths: "error.txt" | exists -%}
-                    <InlineNotification
-                        hideCloseButton
-                        lowContrast
-                        kind="warning"
-                        subtitle={{ casedir | joinpaths: "error.txt" | read | quote }}
-                        />
-                {%- else -%}
-                    <h{{h+2}}>Markers</h{{h+2}}>
-                    <Tabs>
-                        <Tab label="Top 10 genes" />
-                        <Tab label="Table of top 100 genes" />
-                        <TabContent>
-                            {{ table_of_images(glob(casedir, "plots", "*.png"), col = 4) }}
-                        </TabContent>
-                        <TabContent>
-                            <DataTable
-                                src={{ casedir | joinpaths: "markers.txt" | quote }}
-                                data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t", nrows=100 }} }
-                                />
-                        </TabContent>
-                    </Tabs>
-
-                    <h{{h+2}}>Enrichment analysis</h{{h+2}}>
-                    {{ enrichr_report(casedir) }}
-                {%- endif -%}
-            {%- endfor -%}
-        {%- endfor -%}
-    {%- endif -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}