Add Freyja barcode timestamp in report

ahmig · ahmig · commit a6c2fb3cc13d · 2025-07-31T17:06:25.000+02:00
diff --git a/template.qmd b/template.qmd
@@ -42,6 +42,7 @@ params:
   heat_tab: ""
   omega_plot: ""
   name: ""
+  freyja_ts: ""
 output-file: report.html
 ---
 <head>
@@ -100,6 +101,11 @@ if (params$use_bionj) {
 } else {
   dist.tree.algo <- "neighbor-joining (NJ)"
 }
+
+# Freyja timestamp
+freyja.timestamp <- read_file(params$freyja_ts) %>%
+  as.POSIXct(., format = "%m_%d_%Y-%H-%M") %>%
+  strftime(., format = "%d %B %Y at %H:%M")
 ```
 
 ## Summary of the target samples dataset
@@ -141,10 +147,10 @@ table %>%
 
 ### Lineage admixture
 
-The estimated lineage admixture for each sample has been calculated
+The lineage admixture for each sample has been estimated
 using [Freyja](https://github.com/andersen-lab/Freyja).
 
-![Estimated lineage admixture of each sample.
+![Estimated lineage admixture of each sample (Freyja barcode timestamp: `r freyja.timestamp`).
 Samples in the X-axis are ordered chronologically, from more ancient to newer.](`r params$freyja`){#fig-freyja}
 
 ### Phylogenetic reconstruction
diff --git a/workflow/rules/report.smk b/workflow/rules/report.smk
@@ -188,18 +188,19 @@ rule report:
         heat_table = report(REPORT_DIR_TABLES/"figure_10.csv"),
         evo        = report(REPORT_DIR_PLOTS/"figure_11.png"),
         omega_plot = report(REPORT_DIR_PLOTS/"figure_12.png"),
+        freyja_ts  = OUTDIR/"demixing"/"freyja_data"/"last_barcode_update.txt",
         value      = OUTDIR/"diversity.json",
         stats_lm   = OUTDIR/"stats.lm.json",
         table      = OUTDIR/"summary_table.csv",
-        sum_nv     = OUTDIR/"summary_nv.json"
+        sum_nv     = OUTDIR/"summary_nv.json",
     params:
         workflow_version = get_repo_version(BASE_PATH.as_posix(), __version__),
         min_ivar_freq = config["VC"]["IVAR_FREQ"],
         ufboot_reps = config["UFBOOT_REPS"],
         shalrt_reps = config["SHALRT_REPS"],
         name = config["OUTPUT_NAME"],
         use_bionj = config["USE_BIONJ"],
-        cor_method = config["COR"]["METHOD"]
+        cor_method = config["COR"]["METHOD"],
     output:
         html = report(OUTDIR/f"{OUTPUT_NAME}.report.html")
     log:
@@ -233,6 +234,7 @@ rule report:
                 "sum_nv = '{input.sum_nv}', "
                 "heat_tab = '{input.heat_table}', "
                 "omega_plot = '{input.omega_plot}', "
+                "freyja_ts = '{input.freyja_ts}', "
                 "name = '{params.name}'))\" "
-        ">{log} 2>&1 && "
+        ">{log:q} 2>&1 && "
         'mv "$(dirname {input.qmd:q})/report.html" {output.html:q}'
