Run quarto from command line

ahmig · ahmig · commit 2645f3e58691 · 2025-11-05T17:00:56.000+01:00
Also fixes CSS as input
diff --git a/template.qmd b/template.qmd
@@ -4,8 +4,8 @@ subtitle: "Workflow version: `r params$workflow_version`"
 date: last-modified
 date-format: "YYYY-MM-DD"
 title-block-banner: true
-format: 
-  html: 
+format:
+  html:
     page-layout: article
     embed-resources: true
     smooth-scroll: true
@@ -15,36 +15,35 @@ format:
     toc-location: left
     toc-title: Summary
     number-sections: true
-css: "`r params$css`"
+css: __CSSPLACEHOLDER__
 editor: source
 params:
-  css: ""
-  ufboot_reps: ""
-  shalrt_reps: ""
-  min_ivar_freq: ""
-  workflow_version: ""
-  use_bionj: ""
-  cor_method: ""
-  div: ""
-  demix: ""
-  tree: ""
-  tempest: ""
-  SNV: ""
-  SNV_s: ""
-  evo: ""
-  div_value: ""
-  panel: ""
-  volcano: ""
-  tree_ml: ""
-  fig_cor_snp: ""
-  stats_lm: ""
-  stats_ml: ""
-  table: ""
-  sum_nv: ""
-  heat_tab: ""
-  omega_plot: ""
-  name: ""
-  freyja_ts: ""
+  ufboot_reps:
+  shalrt_reps:
+  min_ivar_freq:
+  workflow_version:
+  use_bionj:
+  cor_method:
+  div:
+  demix:
+  tree:
+  tempest:
+  SNV:
+  SNV_s:
+  evo:
+  div_value:
+  panel:
+  volcano:
+  tree_ml:
+  fig_cor_snp:
+  stats_lm:
+  stats_ml:
+  table:
+  sum_nv:
+  heat_tab:
+  omega_plot:
+  name:
+  freyja_ts:
 output-file: report.html
 ---
 <head>
diff --git a/workflow/envs/quarto_render.yaml b/workflow/envs/quarto_render.yaml
@@ -6,5 +6,4 @@ dependencies:
   - quarto==1.8.25
   - deno==2.3.1
   - r-tidyverse==2.0.0
-  - r-quarto==1.5.1
   - r-heatmaply==1.6.0
diff --git a/workflow/rules/report.smk b/workflow/rules/report.smk
@@ -407,7 +407,7 @@ rule summary_table:
 
 rule report:
     conda: "../envs/quarto_render.yaml"
-    shadow: "shallow"
+    shadow: "minimal"
     input:
         qmd        = Path(config["REPORT_QMD"]).resolve(),
         css        = Path(config["REPORT_CSS"]).resolve(),
@@ -443,36 +443,41 @@ rule report:
     log:
         LOGDIR / "report" / "log.txt"
     shell:
-        "set +o pipefail; "
-        "Rscript -e \"quarto::quarto_render("
-            "input = '{input.qmd:q}', "
-            "execute_params=list("
-                "css='{input.css:q}', "
-                "ufboot_reps='{params.ufboot_reps}', "
-                "shalrt_reps='{params.shalrt_reps}', "
-                "min_ivar_freq='{params.min_ivar_freq}', "
-                "workflow_version='{params.workflow_version}', "
-                "use_bionj='{params.use_bionj}', "
-                "cor_method='{params.cor_method}', "
-                "div='{input.diversity}', "
-                "demix ='{input.demix}', "
-                "tree = '{input.tree}', "
-                "tempest = '{input.temest}', "
-                "SNV = '{input.SNV}', "
-                "SNV_s = '{input.SNV_spike}', "
-                "evo = '{input.evo}', "
-                "div_value = '{input.value}', "
-                "panel = '{input.panel}', "
-                "volcano = '{input.volcano}', "
-                "tree_ml = '{input.tree_ml}', "
-                "fig_cor_snp = '{input.fig_cor}', "
-                "stats_lm = '{input.stats_lm}', "
-                "stats_ml = '{input.stats_ml}', "
-                "table = '{input.table}', "
-                "sum_nv = '{input.sum_nv}', "
-                "heat_tab = '{input.heat_table}', "
-                "omega_plot = '{input.omega_plot}', "
-                "freyja_ts = '{input.freyja_ts}', "
-                "name = '{params.name}'))\" "
-        ">{log:q} 2>&1 && "
-        'mv "$(dirname {input.qmd:q})/report.html" {output.html:q}'
+        """
+        set +o pipefail
+        exec >{log} && exec 2>&1
+
+        printf "%s\n" \
+            "ufboot_reps: '{params.ufboot_reps}'" \
+            "shalrt_reps: '{params.shalrt_reps}'" \
+            "min_ivar_freq: '{params.min_ivar_freq}'" \
+            "workflow_version: '{params.workflow_version}'" \
+            "use_bionj: '{params.use_bionj}'" \
+            "cor_method: '{params.cor_method}'" \
+            "div: '{input.diversity}'" \
+            "demix: '{input.demix}'" \
+            "tree: '{input.tree}'" \
+            "tempest: '{input.temest}'" \
+            "SNV: '{input.SNV}'" \
+            "SNV_s: '{input.SNV_spike}'" \
+            "evo: '{input.evo}'" \
+            "div_value: '{input.value}'" \
+            "panel: '{input.panel}'" \
+            "volcano: '{input.volcano}'" \
+            "tree_ml: '{input.tree_ml}'" \
+            "fig_cor_snp: '{input.fig_cor}'" \
+            "stats_lm: '{input.stats_lm}'" \
+            "stats_ml: '{input.stats_ml}'" \
+            "table: '{input.table}'" \
+            "sum_nv: '{input.sum_nv}'" \
+            "heat_tab: '{input.heat_table}'" \
+            "omega_plot: '{input.omega_plot}'" \
+            "freyja_ts: '{input.freyja_ts}'" \
+            "name: '{params.name}'" \
+            >params.yaml
+
+        sed "s|__CSSPLACEHOLDER__|{input.css}|g" {input.qmd:q} >report.qmd
+
+        quarto render report.qmd --execute-params params.yaml
+        mv report.html {output.html:q}
+        """
