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

biopipen/reports/scrna/RadarPlots.svelte

@@ -1,31 +1,15 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 <script>
-    import { Image } from "$libs";
+    import { Image, DataTable } from "$libs";
+    import { Tabs, Tab, TabContent } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=1) -%}
-    {%- set section_file = job.out.outdir | joinpaths: "sections.toml" -%}
-    {%- if section_file | exists -%}
-        {%- set sections = section_file | config: "toml" -%}
-        {%- for section, cases in sections.items() -%}
-            <h{{h}}>{{section | escape}}</h{{h}}>
-            {%- set imgs = [] -%}
-            {%- for case in cases -%}
-                {%- set img = job.out.outdir | joinpaths: case + ".png" -%}
-                {%- set _ = imgs.append(img) -%}
-            {%- endfor -%}
-            {{ table_of_images(imgs) }}
-        {%- endfor -%}
-    {%- else -%}
-        {%- for img in job.out.outdir | glob: "*.png" -%}
-            <h{{h}}>{{img | stem | escape}}</h{{h}}>
-            <Image src={{img | quote}} />
-        {%- endfor -%}
-    {%- endif -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}
-<h1>{{job.in.srtobj | stem}}</h1>
+    <h1>{{job.in.srtobj | stem}}</h1>
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna/ScFGSEA.svelte

@@ -1,35 +1,16 @@
 {% from "utils/gsea.liq" import fgsea_report -%}
 {% from "utils/misc.liq" import report_jobs -%}
 <script>
-    import { Image, DataTable } from "$libs";
+    import { Image, DataTable, Descr } from "$libs";
+    import { Accordion, AccordionItem, 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 -%}
-        {%- for casedir in secdirs | first | glob: "*" -%}
-            {%- if secname == "DEFAULT" -%}
-                <h{{h}}>{{ casedir | basename | escape }}</h{{h}}>
-            {%- else -%}
-                <h{{h}}>{{secname | escape }} - {{ casedir | basename | escape }}</h{{h}}>
-            {%- endif -%}
-            {{ fgsea_report(casedir, h + 1) }}
-        {%- 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}}>
-                {{ fgsea_report(casedir, h + 2) }}
-            {%- 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/SeuratClusterStats.svelte

@@ -1,82 +1,16 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 {% from_ os import path %}
 <script>
-    import { DataTable, Image } from "$libs";
+    import { DataTable, Image, Descr } from "$libs";
     import { Tabs, Tab, TabContent } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=1) -%}
-    {%- set stats_reports_file = job.out.outdir | joinpaths: "stats", "report_toc.json" -%}
-    {%- set features_reports_file = job.out.outdir | joinpaths: "features", "report_toc.json" -%}
-    {%- set dimplots_reports_file = job.out.outdir | joinpaths: "dimplots", "report_toc.json" -%}
-
-    {%- if stats_reports_file | exists -%}
-        {%- set stats = stats_reports_file | config: "json" -%}
-        {% for key, value in stats.items() -%}
-            <h{{h}}>{{key | escape}}</h{{h}}>
-            <Tabs>
-                {% if 'bar' in value -%}
-                    <Tab label="Bar plot" />
-                {% endif -%}
-                {% if 'pie' in value -%}
-                    <Tab label="Pie chart" />
-                {% endif -%}
-                {% if 'table' in value -%}
-                    <Tab label="Table" />
-                {% endif -%}
-                <svelte:fragment slot="content">
-                    {% if 'bar' in value -%}
-                        <TabContent>
-                            <Image src="{{job.out.outdir}}/stats/{{value.bar}}" />
-                        </TabContent>
-                    {% endif -%}
-                    {% if 'pie' in value -%}
-                        <TabContent>
-                            <Image src="{{job.out.outdir}}/stats/{{value.pie}}" />
-                        </TabContent>
-                    {% endif -%}
-                    {% if 'table' in value -%}
-                        <TabContent>
-                            <DataTable src="{{job.out.outdir}}/stats/{{value.table}}"
-                                data={ {{job.out.outdir | joinpaths: "stats", value.table | datatable: sep="\t", nrows=100 }} }
-                                />
-                        </TabContent>
-                    {% endif -%}
-                </svelte:fragment>
-            </Tabs>
-        {%- endfor -%}
-    {%- endif -%}
-
-    {%- if features_reports_file | exists -%}
-        {%- set features = features_reports_file | config: "json" %}
-        {% for key, value in features.items() -%}
-            <h{{h}}>{{key | escape}}</h{{h}}>
-            {% for val in value -%}
-                {% if "name" in val -%}
-                    <h{{h+1}}>{{val.name | escape}}</h{{h+1}}>
-                {%- endif -%}
-                {% if val.kind == "table" -%}
-                    <DataTable src="{{job.out.outdir}}/features/{{val.file}}"
-                        data={ {{job.out.outdir | joinpaths: "features", val.file | datatable: sep="\t", nrows=100 }} }
-                        />
-                {% else -%}
-                    <Image src="{{job.out.outdir}}/features/{{val.file}}" />
-                {% endif -%}
-            {%- endfor -%}
-        {%- endfor -%}
-    {%- endif -%}
-
-    {%- if dimplots_reports_file | exists -%}
-        {%- set dimplots = dimplots_reports_file | config: "json" %}
-        {% for key, value in dimplots.items() -%}
-            <h{{h}}>{{key | escape}}</h{{h}}>
-            <Image src="{{job.out.outdir}}/dimplots/{{value}}" />
-        {%- endfor -%}
-    {%- endif -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}
-<h1>{{job.in.srtobj | stem}}</h1>
+    <h1>{{job.in.srtobj | stem}}</h1>
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna/SeuratPreparing.svelte

@@ -1,34 +1,11 @@
-{% from "utils/misc.liq" import report_jobs, table_of_images -%}
+{% from "utils/misc.liq" import report_jobs -%}
 {% from_ os import path %}
 <script>
-    import { Image, DataTable } from "$libs";
-    import { Tile } from "$ccs";
+    import { Image, DataTable, Descr } from "$libs";
 </script>
 
 {%- macro report_job(job, h=1) -%}
-    <h{{h}}>Applied filters</h{{h}}>
-    <Tile>
-        <p>Cell filters: {{envs.cell_qc | str | escape}}</p>
-        <p>Gene filters: {{
-            proc.envs.gene_qc
-            | str
-            | replace: "{", "&#123"
-            | replace: "}", "&#125"
-        }}</p>
-
-        <DataTable
-            src={{job.outdir | joinpaths: 'plots', 'dim.txt' | quote}}
-            data={ {{job.outdir | joinpaths: 'plots', 'dim.txt' | datatable: sep="\t"}} } />
-    </Tile>
-
-    <h{{h}}>Violin plots</h{{h}}>
-    {% set qcimgs = job.outdir | glob: "plots", "*.vln.png" %}
-    {{ table_of_images(qcimgs) }}
-
-    <h{{h}}>Scatter plots</h{{h}}>
-    {% set qcimgs = job.outdir | glob: "plots", "*.scatter.png" %}
-    {{ table_of_images(qcimgs) }}
-
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}

biopipen/reports/scrna/TopExpressingGenes.svelte

@@ -1,51 +1,13 @@
 {% 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 "$libs";
+    import { Accordion, AccordionItem, Tabs, Tab, TabContent } from "$ccs";
 </script>
 
 
 {%- macro report_job(job, h=1) -%}
-    {%- set secdirs = job.out.outdir | glob: "*" -%}
-    {%- if len(secdirs) == 1 -%}
-        {%- set secname = secdirs | first | basename -%}
-        {%- 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 -%}
-
-            <h{{h+1}}>Markers</h{{h+1}}>
-            <DataTable
-                src={{ casedir | joinpaths: "exprn.txt" | quote }}
-                data={ {{ casedir | joinpaths: "exprn.txt" | datatable: sep="\t", nrows=100 }} }
-                />
-
-            <h{{h+1}}>Enrichment analysis</h{{h+1}}>
-            {{ enrichr_report(casedir) }}
-
-        {%- 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}}>
-
-                <h{{h+2}}>Markers</h{{h+2}}>
-                <DataTable
-                    src={{ casedir | joinpaths: "exprn.txt" | quote }}
-                    data={ {{ casedir | joinpaths: "exprn.txt" | datatable: sep="\t", nrows=100 }} }
-                    />
-
-                <h{{h+2}}>Enrichment analysis</h{{h+2}}>
-                {{ enrichr_report(casedir) }}
-
-            {%- endfor -%}
-        {%- endfor -%}
-    {%- endif -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}

biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte

@@ -2,26 +2,27 @@
 {% from "utils/gsea.liq" import fgsea_report_script, fgsea_report, gsea_report -%}
 
 <script>
-{{ fgsea_report_script() }}
+  import { Image, DataTable, Descr } from "$libs";
+  import { Tabs, Tab, TabContent, Accordion, AccordionItem } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=2) -%}
-  {%- for ssdir in job.out.outdir | glob: "*" -%}
-    {%- if basename(ssdir) == "ALL" -%}
-      {%- set h = 1 -%}
-    {%- else -%}
-      <h{{h}}>{{ ssdir | stem }}</h{{h}}>
-    {%- endif -%}
+  {% if envs.fgsea %}
+    {{ job | render_job: h=h }}
+  {% else %}
+    {%- for ssdir in job.out.outdir | glob: "*" -%}
+      {%- if basename(ssdir) == "ALL" -%}
+        {%- set h = 1 -%}
+      {%- else -%}
+        <h{{h}}>{{ ssdir | stem }}</h{{h}}>
+      {%- endif -%}
 
-    {% for cldir in ssdir | glob: '*' %}
-      <h{{h+1}}>{{ cldir | basename }}</h{{h+1}}>
-      {% if envs.fgsea %}
-          {{ fgsea_report(cldir, h+2, envs, envs.top) }}
-      {% else %}
-          {{ gsea_report(cldir, h+2, envs, envs.top) }}
-      {% endif %}
-    {% endfor %}
-  {%- endfor -%}
+      {% for cldir in ssdir | glob: '*' %}
+        <h{{h+1}}>{{ cldir | basename }}</h{{h+1}}>
+        {{ gsea_report(cldir, h+2, envs, envs.top) }}
+      {% endfor %}
+    {%- endfor -%}
+  {% endif %}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}

biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.svelte

@@ -2,26 +2,23 @@
 {% from "utils/gsea.liq" import fgsea_report, gsea_report -%}
 
 <script>
-  import { Image, DataTable } from "$libs";
+  import { Image, DataTable, Descr } from "$libs";
+  import { Tabs, Tab, TabContent, Accordion, AccordionItem } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=2) -%}
-  {%  for groupdir in job.out.outdir | glob: "*" %}
-    <h{{h}}>{{groupdir | basename}}</h{{h}}>
-    {%- set dsdirs = groupdir | glob: "*" -%}
-    {% for dsdir in groupdir | glob: "*" %}
-        <h{{h+1}}>{{ dsdir | basename }}</h{{h+1}}>
-        {% if envs.fgsea %}
-            {% if dsdir | joinpaths: "fgsea.txt" | isfile %}
-                {{ fgsea_report(dsdir, h+2, envs, envs.top) }}
-            {% else %}
-                <p>Not enough events.</p>
-            {% endif %}
-        {% else %}
-            {{ gsea_report(dsdir, h+2, envs, envs.top) }}
-        {% endif %}
+  {% if envs.fgsea %}
+    {{ job | render_job: h=h }}
+  {% else %}
+    {%  for groupdir in job.out.outdir | glob: "*" %}
+      <h{{h}}>{{groupdir | basename}}</h{{h}}>
+      {%- set dsdirs = groupdir | glob: "*" -%}
+      {% for dsdir in groupdir | glob: "*" %}
+          <h{{h+1}}>{{ dsdir | basename }}</h{{h+1}}>
+          {{ gsea_report(dsdir, h+2, envs, envs.top) }}
+      {% endfor %}
     {% endfor %}
-  {% endfor %}
+  {% endif %}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}

biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte

@@ -1,48 +1,58 @@
 {% from "utils/misc.liq" import report_jobs -%}
 
 <script>
-    import { Image } from "$libs";
+    import { Image, Descr } from "$libs";
+    import { ListItem, UnorderedList } from "$ccs";
 </script>
 
 <h1>Introduction</h1>
 
-<div class="markdown-wrap">
-<Markdown>
+<Descr>
+    Metabolic landscape of single cells in the tumor microenvironment.
+</Descr>
 
-Metabolic landscape of single cells in the tumor microenvironment.
-
-## Workflow of the original analysis
+<h2>Workflow of the original analysis</h2>
 <Image src="https://github.com/LocasaleLab/Single-Cell-Metabolic-Landscape/raw/master/pipeline.png" />
 
-## Reference
-- [Xiao, Zhengtao, Ziwei Dai, and Jason W. Locasale. "Metabolic landscape of the tumor microenvironment at single cell resolution." Nature communications 10.1 (2019): 1-12.](https://www.nature.com/articles/s41467-019-11738-0)
-- [Original pipeline](https://github.com/LocasaleLab/Single-Cell-Metabolic-Landscape)
-
-## Analyses with this pipeline
-
+<h2>Reference</h2>
+<UnorderedList>
+    <ListItem><a href="https://www.nature.com/articles/s41467-019-11738-0" target="_blank">
+        Zhengtao, Ziwei Dai, and Jason W. Locasale.
+        "Metabolic landscape of the tumor microenvironment at single cell resolution."
+        Nature communications 10.1 (2019): 1-12.
+    </a></ListItem>
+    <ListItem><a href="https://github.com/LocasaleLab/Single-Cell-Metabolic-Landscape" target="_blank">
+        Orginal pipeline
+    </a></ListItem>
+</UnorderedList>
+
+<h2>Analyses with this pipeline</h2>
+
+<Descr>
 The cells are grouped at 2 dimensions: `grouping`, usually the cell types, and `subsetting`, usually
 the groups that bring biological meaning (i.e. different timepoints or sample types (tumor/normal)).
+</Descr>
+
+<UnorderedList>
+<ListItem>
+    MetabolicPathwayActivity (this page)
+    <p>Investigating the metabolic pathways of the cells in different groups and subsets.</p>
+    <p>The cells are first grouped by subsets and then the metabolic activities are examined for each groups in different subsets.</p>
+</ListItem>
+<ListItem>
+    <a href="../MetabolicPathwayHeterogeneity/index.html">MetabolicPathwayHeterogeneity</a>
+    <p>Showing metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities</p>
+</ListItem>
+<ListItem>
+    <a href="../MetabolicFeatures/index.html">MetabolicFeatures</a>
+    <p>Gene set enrichment analysis against the metabolic pathways for groups in different subsets.</p>
+</ListItem>
+<ListItem>
+    <a href="../MetabolicFeaturesIntraSubsets/index.html">MetabolicFeaturesIntraSubsets</a>
+    <p>Gene set enrichment analysis against the metabolic pathways for subsets in different groups.</p>
+</ListItem>
+</UnorderedList>
 
-- **MetabolicPathwayActivity (this page)**
-
-    Investigating the metabolic pathways of the cells in different groups and subsets.
-
-    The cells are first grouped by subsets and then the metabolic activities are examined for each groups in different subsets.
-
-- **MetabolicPathwayHeterogeneity**
-
-    Showing metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities
-
-- **MetabolicFeatures**
-
-    Gene set enrichment analysis against the metabolic pathways for groups in different subsets.
-
-- **MetabolicFeaturesIntraSubsets** (optional)
-
-    Gene set enrichment analysis against the metabolic pathways for subsets based on the designed comparison in different groups.
-
-</Markdown>
-</div>
 
 {%- macro report_job(job, h=2) -%}
   {%- for ssdir in job.out.outdir | glob: "*" -%}
@@ -51,10 +61,10 @@ the groups that bring biological meaning (i.e. different timepoints or sample ty
   {%- endif -%}
   <h{{h}}>{{ ssdir | stem }}</h{{h}}>
 
-  <h{{ h+1 }}>Metabolic pathway activities by {{envs.grouping}}</h{{ h+1 }}>
+  <h{{ h+1 }}>Metabolic pathway activities by <code>{{envs.grouping}}</code></h{{ h+1 }}>
   <Image src="{{ssdir | joinpaths: 'KEGGpathway_activity_heatmap.png'}}" />
 
-  <h{{ h+1 }}>Distributions of pathway activities by {{envs.grouping}}</h{{ h+1 }}>
+  <h{{ h+1 }}>Distributions of pathway activities by <code>{{envs.grouping}}</code></h{{ h+1 }}>
   <Image src="{{ssdir | joinpaths: 'pathway_activity_violinplot.png'}}" />
   {%- endfor -%}
 
@@ -77,21 +87,3 @@ the groups that bring biological meaning (i.e. different timepoints or sample ty
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}
-
-<style>
-
-.markdown-wrap ul {
-    list-style-position: inside;
-    list-style-type: disc;
-    margin-top: 0.2rem;
-}
-
-.markdown-wrap ul li p {
-    padding-left: 1.2rem;
-}
-
-.markdown-wrap ul li > p:first-of-type {
-    padding-left: 0;
-    display: inline;
-}
-</style>

biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte

@@ -1,17 +1,11 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 
 <script>
-    import { Image } from "$libs";
+    import { Image, Descr } from "$libs";
 </script>
 
 {%- macro report_job(job, h=2) -%}
-  {%- for ssdir in job.out.outdir | glob: "*" -%}
-  <h{{h}}>{{ ssdir | stem }}</h{{h}}>
-
-  <h{{h+1}}>Metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities</h{{h+1}}>
-  <Image src="{{ssdir | joinpaths: 'pathway_heterogeneity.png'}}" />
-
-  {%- endfor -%}
+  {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}

biopipen/reports/tcr/CDR3AAPhyschem.svelte

@@ -1,67 +1,28 @@
 {% from "utils/misc.liq" import report_jobs -%}
 <script>
-    import { Image, DataTable } from "$libs";
+    import { Image, DataTable, Descr } from "$libs";
     import { Tile, UnorderedList, ListItem, Link, Tabs, Tab, TabContent } from "$ccs";
 </script>
 
-
-{%- macro report_job(job, h=1) -%}
-
-    <h{{h}}>Summary</h{{h}}>
-    <Tile>
-        The idea is to perform a regression between two groups of cells
-        (e.g. Treg vs Tconv) at different length of CDR3 AA sequences.
-        The regression will be performed for each physicochemical feature of the
-        AA (hydrophobicity, volume and isolectric point).
-    </Tile>
-
-    <h{{h+1}}>Reference</h{{h+1}}>
-    <UnorderedList style="padding-left: 1rem">
-        <ListItem class="ccs-li"><Link href="https://www.nature.com/articles/ni.3491" target="_blank">https://www.nature.com/articles/ni.3491</Link></ListItem>
-        <ListItem class="ccs-li"><Link href="https://www.nature.com/articles/s41590-022-01129-x" target="_blank">https://www.nature.com/articles/s41590-022-01129-x</Link></ListItem>
-        <ListItem class="ccs-li">Wimley, W. C. &amp; White, S. H. Experimentally determined hydrophobicity scale for proteins at membrane - interfaces. Nat. Struct. Biol. 3, 842-848 (1996).</ListItem>
-        <ListItem class="ccs-li">Hdbk of chemistry &amp; physics 72nd edition. (CRC Press, 1991).</ListItem>
-        <ListItem class="ccs-li">Zamyatnin, A. A. Protein volume in solution. Prog. Biophys. Mol. Biol. 24, 107-123 (1972).</ListItem>
+<h1>Summary</h1>
+<Descr>
+    The idea is to perform a regression between two groups of cells
+    (e.g. Treg vs Tconv) at different length of CDR3 AA sequences.
+    The regression will be performed for each physicochemical feature of the
+    AA (hydrophobicity, volume and isolectric point).
+
+    <h2>Reference</h2>
+    <UnorderedList>
+        <ListItem><Link href="https://www.nature.com/articles/ni.3491" target="_blank">https://www.nature.com/articles/ni.3491</Link></ListItem>
+        <ListItem><Link href="https://www.nature.com/articles/s41590-022-01129-x" target="_blank">https://www.nature.com/articles/s41590-022-01129-x</Link></ListItem>
+        <ListItem>Wimley, W. C. &amp; White, S. H. Experimentally determined hydrophobicity scale for proteins at membrane - interfaces. Nat. Struct. Biol. 3, 842-848 (1996).</ListItem>
+        <ListItem>Hdbk of chemistry &amp; physics 72nd edition. (CRC Press, 1991).</ListItem>
+        <ListItem>Zamyatnin, A. A. Protein volume in solution. Prog. Biophys. Mol. Biol. 24, 107-123 (1972).</ListItem>
     </UnorderedList>
+</Descr>
 
-    <h{{h}}>Available Cells</h{{h}}>
-    <DataTable
-        src={{job.out.outdir | joinpaths: "stats.txt" | quote}}
-        data={ {{job.out.outdir | joinpaths: "stats.txt" | datatable: sep="\t", index_col=None}} }
-        />
-
-    {% for subsetdir in job.out.outdir | glob: "*" %}
-        {% if not subsetdir | isdir %}
-            {% continue %}
-        {% endif %}
-        {% if basename(subsetdir) == "ALL" %}
-            {% set h = h - 1 %}
-        {% else %}
-            <h{{h}}>Subset: {{subsetdir | stem}}</h{{h}}>
-        {% endif %}
-
-        <h{{h+1}}>Estimated OR (per s.d.) for each physicochemical feature</h{{h+1}}>
-        <Tabs>
-            <Tab label="Plot" />
-            <Tab label="Table" />
-            <svelte:fragment slot="content">
-                <TabContent>
-                    <Image src={{subsetdir | joinpaths: "estimated_coefficients.png" | quote}} />
-                </TabContent>
-                <TabContent>
-                    <DataTable
-                        src={{subsetdir | joinpaths: "estimates.txt" | quote}}
-                        data={ {{subsetdir | joinpaths: "estimates.txt" | datatable: sep="\t", index_col=None}} }
-                        />
-                </TabContent>
-            </svelte:fragment>
-        </Tabs>
-
-        <h{{h+1}}>Hydrophobicity Distribution</h{{h+1}}>
-        <Image src={{subsetdir | joinpaths: "distribution.png" | quote}} />
-
-    {% endfor %}
-
+{%- macro report_job(job, h=1) -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}
@@ -69,11 +30,3 @@
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}
-
-<style>
-:global(.ccs-li) {
-    /* default will have messy bullet points */
-    list-style-type: square;
-    position: unset !important;
-}
-</style>