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

biopipen/scripts/scrna/SeuratPreparing.R

@@ -5,6 +5,7 @@ library(future)
 library(bracer)
 library(ggplot2)
 library(tidyseurat)
+library(slugify)
 
 metafile = {{in.metafile | quote}}
 rdsfile = {{out.rdsfile | quote}}
@@ -15,6 +16,18 @@ set.seed(8525)
 options(future.globals.maxSize = 80000 * 1024^2)
 plan(strategy = "multicore", workers = envs$ncores)
 
+add_report(
+    list(
+        kind = "descr",
+        name = "Filters applied",
+        content = paste0(
+            "<p>Cell filters: ", html_escape(envs$cell_qc), "</p>",
+            "<p>Gene filters: ", html_escape(envs$gene_qc), "</p>"
+        )
+    ),
+    h1 = "Filters and QC"
+)
+
 metadata = read.table(
     metafile,
     header = TRUE,
@@ -57,7 +70,7 @@ rename_files = function(e, sample, path) {
 }
 
 load_sample = function(sample) {
-    print(paste("  Loading sample:", sample, "..."))
+    log_info("- Loading sample: {sample} ...")
     mdata = as.data.frame(metadata)[metadata$Sample == sample, , drop=TRUE]
     path = as.character(mdata$RNAData)
     if (is.na(path) || !is.character(path) || nchar(path) == 0) {
@@ -105,10 +118,10 @@ load_sample = function(sample) {
 # Load data
 samples = as.character(metadata$Sample)
 
-print("- Reading samples individually ...")
+log_info("Reading samples individually ...")
 obj_list = lapply(samples, load_sample)
 
-print("- Merging samples ...")
+log_info("Merging samples ...")
 if (length(obj_list) >= 2) {
     y = c()
     for (i in 2:length(obj_list)) y = c(y, obj_list[[i]])
@@ -117,7 +130,7 @@ if (length(obj_list) >= 2) {
     sobj = obj_list[[1]]
 }
 
-print("- Adding metadata for QC ...")
+log_info("Adding metadata for QC ...")
 sobj$percent.mt = PercentageFeatureSet(sobj, pattern = "^MT-")
 sobj$percent.ribo = PercentageFeatureSet(sobj, pattern = "^RP[SL]")
 sobj$percent.hb = PercentageFeatureSet(sobj, pattern = "^HB[^(P)]")
@@ -126,7 +139,7 @@ sobj$percent.plat = PercentageFeatureSet(sobj, pattern = "PECAM1|PF4")
 dim_df = data.frame(When = "Before_QC", nCells = ncol(sobj), nGenes = nrow(sobj))
 
 if (is.null(envs$cell_qc) || length(envs$cell_qc) == 0) {
-    warning("No cell QC criteria is provided. All cells will be kept.", immediate. = TRUE)
+    log_warn("No cell QC criteria is provided. All cells will be kept.")
     envs$cell_qc = "TRUE"
 }
 
@@ -136,9 +149,21 @@ plotsdir = file.path(joboutdir, "plots")
 dir.create(plotsdir, showWarnings = FALSE)
 
 # Violin plots
-print("- Plotting violin plots ...")
+log_info("Plotting violin plots ...")
+add_report(
+    list(
+        kind = "descr",
+        content = paste(
+            "The violin plots for each feature. The cells are grouped by sample.",
+            "The cells that fail the QC criteria are colored in red, and",
+            "the cells that pass the QC criteria are colored in black.",
+            "The cells that fail the QC criteria are filtered out in the returned Seurat object."
+        )
+    ),
+    h1 = "Violin Plots"
+)
 for (feat in feats) {
-    print(paste0("  ", feat, "..."))
+    log_info("- For feature: {feat}")
     vln_p = VlnPlot(
         sobj,
         cols = rep("white", length(samples)),
@@ -150,20 +175,43 @@ for (feat in feats) {
             aes(color = .QC),
             data = vln_p$data,
             position = position_jitterdodge(jitter.width = 0.4, dodge.width = 0.9)
-        ) + scale_color_manual(values = c("black", "red"), breaks = c(TRUE, FALSE))
+        ) + scale_color_manual(values = c("#181818", pal_biopipen()(1)), breaks = c(TRUE, FALSE))
 
+    vlnplot = file.path(plotsdir, paste0(slugify(feat, tolower = FALSE), ".vln.png"))
     png(
-        file.path(plotsdir, paste0(feat, ".vln.png")),
+        vlnplot,
         width = 800 + length(samples) * 15, height = 600, res = 100
     )
     print(vln_p)
     dev.off()
+
+    add_report(
+        list(
+            src = vlnplot,
+            name = feat,
+            descr = paste0("Distribution of ", feat, " for each sample.")
+        ),
+        h1 = "Violin Plots",
+        ui = "table_of_images"
+    )
 }
 
 # Scatter plots against nCount_RNA
-print("- Plotting scatter plots ...")
+log_info("Plotting scatter plots ...")
+add_report(
+    list(
+        kind = "descr",
+        content = paste(
+            "The scatter plots for each feature against nCount_RNA. ",
+            "The cells that fail the QC criteria are colored in red, and",
+            "the cells that pass the QC criteria are colored in black.",
+            "The cells that fail the QC criteria are filtered out in the returned Seurat object."
+        )
+    ),
+    h1 = "Scatter Plots"
+)
 for (feat in setdiff(feats, "nCount_RNA")) {
-    print(paste0("  ", feat, "..."))
+    log_info("- For feature: {feat}, against nCount_RNA")
     scat_p = FeatureScatter(
         sobj,
         feature1 = "nCount_RNA",
@@ -171,22 +219,30 @@ for (feat in setdiff(feats, "nCount_RNA")) {
         group.by = ".QC"
     ) +
     NoLegend() +
-    scale_color_manual(values = c("black", "red"), breaks = c(TRUE, FALSE))
+    scale_color_manual(values = c("#181818", pal_biopipen()(1)), breaks = c(TRUE, FALSE))
 
-    png(
-        file.path(plotsdir, paste0(feat, "-nCount_RNA.scatter.png")),
-        width = 800, height = 600, res = 100
-    )
+    scatfile = file.path(plotsdir, paste0(slugify(feat, tolower = FALSE), "-nCount_RNA.scatter.png"))
+    png(scatfile, width = 800, height = 600, res = 100)
     print(scat_p)
     dev.off()
+
+    add_report(
+        list(
+            src = scatfile,
+            name = paste0(feat, " vs nCount_RNA"),
+            descr = paste0("Scatter plot for ", feat, " against nCount_RNA")
+        ),
+        h1 = "Scatter Plots",
+        ui = "table_of_images"
+    )
 }
 
 # Do the filtering
-print("- Filtering cells ...")
+log_info("Filtering cells using QC criteria ...")
 sobj = sobj %>% filter(.QC)
 sobj$.QC = NULL
 
-print("- Filtering genes ...")
+log_info("Filtering genes ...")
 if (is.list(envs$gene_qc)) {
     if ("min_cells" %in% names(envs$gene_qc)) {
         genes = rownames(sobj)[Matrix::rowSums(sobj) >= envs$gene_qc$min_cells]
@@ -202,8 +258,26 @@ dim_df = rbind(
     )
 )
 
+log_info("Saving dimension table ...")
 write.table(dim_df, file = file.path(plotsdir, "dim.txt"),
             row.names = FALSE, quote = FALSE, sep = "\t")
 
-print("- Saving results ...")
+add_report(
+    list(
+        kind = "descr",
+        content = paste(
+            "The dimension table for the Seurat object. The table contains the number of cells and genes before and after QC."
+        )
+    ),
+    list(
+        kind = "table",
+        data = list(path = file.path(plotsdir, "dim.txt"))
+    ),
+    h1 = "Filters and QC"
+)
+
+
+log_info("Saving filtered seurat object ...")
 saveRDS(sobj, rdsfile)
+
+save_report(joboutdir)

biopipen/scripts/scrna/TopExpressingGenes.R

@@ -5,11 +5,14 @@ library(tibble)
 library(enrichR)
 library(rlang)
 library(dplyr)
+library(slugify)
+library(ggprism)
 
 setEnrichrSite("Enrichr")
 
 srtfile <- {{in.srtobj | r}}
 outdir <- {{out.outdir | r}}
+joboutdir <- {{job.outdir | r}}
 mutaters <- {{ envs.mutaters | r }}
 ident <- {{ envs.ident | r }}
 group.by <- {{ envs["group-by"] | r }}  # nolint
@@ -22,16 +25,16 @@ cases <- {{ envs.cases | r: todot = "-" }}  # nolint
 
 set.seed(8525)
 
-print("- Loading Seurat object ...")
+log_info("Loading Seurat object ...")
 srtobj <- readRDS(srtfile)
 
-print("- Mutate meta data if needed ...")
+log_info("Mutate meta data if needed ...")
 if (!is.null(mutaters) && length(mutaters)) {
     srtobj@meta.data <- srtobj@meta.data %>%
         mutate(!!!lapply(mutaters, parse_expr))
 }
 
-print("- Expanding cases ...")
+log_info("Expanding cases ...")
 if (is.null(cases) || length(cases) == 0) {
     cases <- list(
         DEFAULT = list(
@@ -61,11 +64,14 @@ if (is.null(cases) || length(cases) == 0) {
 
 # Expand each and ident
 newcases <- list()
+sections <- c()
 for (name in names(cases)) {  # nolint
     case <- cases[[name]]
     if (is.null(case$each) && !is.null(case$ident)) {
+        sections <- c(sections, case$section)
         newcases[[paste0(case$section, ":", name)]] <- case
     } else if (is.null(case$each)) {
+        sections <- c(sections, name)
         idents <- srtobj@meta.data %>%
             pull(case$group.by) %>%
             unique() %>%
@@ -93,15 +99,21 @@ for (name in names(cases)) {  # nolint
                     na.omit()
                 for (ident in idents) {
                     kname <- if (name == "DEFAULT") "" else paste0("-", name)
+                    sections <- c(sections, paste0(each, kname))
                     key <- paste0(each, kname, ":", ident)
                     if (case$prefix_each) {
-                        key <- paste0(case$each, "-", key)
+                        key <- paste0(
+                            ifelse(case$each == "seurat_clusters", "Cluster", case$each),
+                            " - ",
+                            key
+                        )
                     }
                     newcases[[key]] <- case
                     newcases[[key]]$ident <- ident
                     newcases[[key]]$group.by <- by  # nolint
                 }
             } else {
+                sections <- c(sections, case$each)
                 key <- paste0(case$each, ":", each)
                 if (name != "DEFAULT") {
                     key <- paste0(key, " - ", name)
@@ -112,11 +124,33 @@ for (name in names(cases)) {  # nolint
     }
 }
 cases <- newcases
+single_section <- length(unique(sections)) == 1
+
+casename_info <- function(casename, create = FALSE) {
+    sec_case_names <- strsplit(casename, ":")[[1]]
+    cname <- paste(sec_case_names[-1], collapse = ":")
+
+    out <- list(
+        casename = casename,
+        section = sec_case_names[1],
+        case = cname,
+        section_slug = slugify(sec_case_names[1], tolower = FALSE),
+        case_slug = slugify(cname, tolower = FALSE)
+    )
+    out$casedir <- file.path(outdir, out$section_slug, out$case_slug)
+    if (create) {
+        dir.create(out$casedir, showWarnings = FALSE, recursive = TRUE)
+    }
+    out
+}
 
 do_enrich <- function(expr, odir) {
-    print("  Saving expressions ...")
+    log_info("  Saving expressions ...")
+    expr <- expr %>% as.data.frame()
+    colnames(expr) <- c("Expression")
+    expr <- expr %>% rownames_to_column("Gene") %>% select(Gene, Expression)
     write.table(
-        expr %>% as.data.frame() %>% rownames_to_column("Gene"),
+        expr,
         file.path(odir, "expr.txt"),
         sep = "\t",
         row.names = TRUE,
@@ -124,7 +158,7 @@ do_enrich <- function(expr, odir) {
         quote = FALSE
     )
     write.table(
-        expr %>% as.data.frame() %>% rownames_to_column("Gene") %>% head(n),
+        expr %>% head(n),
         file.path(odir, "exprn.txt"),
         sep = "\t",
         row.names = TRUE,
@@ -132,8 +166,8 @@ do_enrich <- function(expr, odir) {
         quote = FALSE
     )
 
-    print("  Running enrichment ...")
-    enriched <- enrichr(rownames(head(expr, n)), dbs)  # nolint
+    log_info("  Running enrichment ...")
+    enriched <- enrichr(head(expr$Gene, n), dbs)  # nolint
     for (db in dbs) {
         write.table(
             enriched[[db]],
@@ -147,29 +181,77 @@ do_enrich <- function(expr, odir) {
             file.path(odir, paste0("Enrichr-", db, ".png")),
             res = 100, height = 1000, width = 1000
         )
-        print(plotEnrich(enriched[[db]], showTerms = 20, title = db))  # nolint
+        print(
+            plotEnrich(enriched[[db]], showTerms = 20, title = db) +
+            theme_prism()
+        )
         dev.off()
     }
 }
 
 do_case <- function(casename) {
-    print(paste("- Running for case:", casename))
+    log_info("- Running for case: {casename} ...")
     case <- cases[[casename]]
-    parts <- unlist(strsplit(casename, ":"))
-    section <- parts[1]
-    casename <- paste(parts[-1], collapse = ":")
+    info <- casename_info(casename, create = TRUE)
 
-    print("  Calculating average expression ...")
+    log_info("  Calculating average expression ...")
     avgexpr <- AverageExpression(
         srtobj,
         group.by = case$group.by
     )$RNA[, case$ident, drop = FALSE]
     avgexpr <- avgexpr[order(-avgexpr), , drop = FALSE]
 
-    odir <- file.path(outdir, section, casename)
-    dir.create(odir, recursive = TRUE, showWarnings = FALSE)
+    do_enrich(avgexpr, info$casedir)
+
+    add_case_report(info)
+}
 
-    do_enrich(avgexpr, odir)
+add_case_report <- function(info) {
+    log_info("  Adding case report ...")
+    h1 = ifelse(
+        info$section == "DEFAULT",
+        info$case,
+        ifelse(
+            single_section,
+            paste0(
+                ifelse(info$section == "seurat_clusters", "Cluster", info$section),
+                " - ",
+                info$case
+            ),
+            info$section
+        )
+    )
+    h2 = ifelse(
+        info$section == "DEFAULT",
+        "#",
+        ifelse(single_section, "#", info$case)
+    )
+
+    add_report(
+        list(
+            kind = "descr",
+            content = paste0("Top ", n, " expressing genes")
+        ),
+        list(
+            kind = "table",
+            src = file.path(info$casedir, "exprn.txt")
+        ),
+        h1 = h1,
+        h2 = ifelse(h2 == "#", "Top Expressing Genes", h2),
+        h3 = ifelse(h2 == "#", "#", "Top Expressing Genes")
+    )
+
+    add_report(
+        list(
+            kind = "descr",
+            content = paste0("Enrichment analysis for the top ", n, " expressing genes")
+        ),
+        list(kind = "enrichr", dir = info$casedir),
+        h1 = h1,
+        h2 = ifelse(h2 == "#", "Enrichment Analysis", h2),
+        h3 = ifelse(h2 == "#", "#", "Enrichment Analysis")
+    )
 }
 
 sapply(sort(names(cases)), do_case)
+save_report(joboutdir)

biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R

@@ -1,10 +1,13 @@
+source("{{biopipen_dir}}/utils/misc.R")
 source("{{biopipen_dir}}/utils/gsea.R")
 
 library(parallel)
 library(Seurat)
+library(slugify)
 
 sobjfile <- {{ in.sobjfile | r }}
 outdir <- {{ out.outdir | r }}
+joboutdir <- {{ job.outdir | r }}
 gmtfile <- {{ envs.gmtfile | r }}
 ncores <- {{ envs.ncores | r }}
 fgsea <- {{ envs.fgsea | r }}
@@ -37,10 +40,10 @@ pathways <- gmt_pathways(gmtfile)
 metabolics <- unique(as.vector(unname(unlist(pathways))))
 sobj <- readRDS(sobjfile)
 
-do_one_group <- function(obj, group, outputdir) {
-    print(paste("- Processing group", grouping, ":", group))
+do_one_group <- function(obj, group, outputdir, h1) {
+    log_info(paste("- Processing group", grouping, ":", group))
     groupname = paste0(grouping_prefix, group)
-    odir = file.path(outputdir, groupname)
+    odir = file.path(outputdir, slugify(groupname, tolower = FALSE))
     dir.create(odir, showWarnings = FALSE)
 
     classes = as.character(obj@meta.data[[grouping]])
@@ -65,19 +68,24 @@ do_one_group <- function(obj, group, outputdir) {
         }
     }, error=function(e) {
         unlink(odir, recursive = T, force = T)
-        warning(paste("Unable to run for", group))
-        warning(e)
+        log_warn(paste("Unable to run for", group))
+        log_warn(e)
     })
 
+    add_report(
+        list(kind = "fgsea", dir = odir),
+        h1 = ifelse(is.null(h1), groupname, h1),
+        h2 = ifelse(is.null(h1), "#", groupname)
+    )
 }
 
 do_one_subset <- function(s, subset_col, subset_prefix) {
-    print(paste("Processing subset", subset_col, ":", s))
+    log_info(paste("Processing subset", subset_col, ":", s))
     if (is.null(s)) {
         outputdir <- file.path(outdir, "ALL")
         subset_obj <- sobj
     } else {
-        outputdir <- file.path(outdir, paste0(subset_prefix, s))
+        outputdir <- file.path(outdir, slugify(paste0(subset_prefix, s), tolower = FALSE))
         subset_code <- paste0("subset(sobj, subset = ", subset_col, "=='", s, "')")
         subset_obj <- eval(parse(text = subset_code))
     }
@@ -85,9 +93,13 @@ do_one_subset <- function(s, subset_col, subset_prefix) {
 
     subset_obj <- subset(subset_obj, features = intersect(rownames(subset_obj), metabolics))
 
+    h1 <- NULL
+    if (!is.null(s)) {
+        h1 <- paste0(subset_prefix, s)
+    }
     groups = subset_obj@meta.data[[grouping]]
     x = mclapply(as.character(unique(groups)), function(group) {
-        do_one_group(subset_obj, group, outputdir)
+        do_one_group(subset_obj, group, outputdir, h1)
     }, mc.cores = ncores)
     if (any(unlist(lapply(x, class)) == "try-error")) {
         stop("mclapply error")
@@ -110,3 +122,4 @@ if (is.null(subsetting_cols)) {
     }
 }
 
+save_report(joboutdir)

biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R

@@ -4,9 +4,11 @@ source("{{biopipen_dir}}/utils/gsea.R")
 library(parallel)
 library(scater)
 library(Seurat)
+library(slugify)
 
 sobjfile <- {{ in.sobjfile | r }}
 outdir <- {{ out.outdir | r }}
+joboutdir <- {{ job.outdir | r }}
 gmtfile <- {{ envs.gmtfile | r }}
 ncores <- {{ envs.ncores | r }}
 fgsea <- {{ envs.fgsea | r }}
@@ -47,7 +49,8 @@ do_one_comparison <- function(
     control,
     groupdir,
     subset_col,
-    subset_prefix
+    subset_prefix,
+    groupname
 ) {
     print(paste("  Design:", compname, "(", case, ",", control, ")"))
     case_code = paste0("subset(obj, subset = ", subset_col, " == '", case, "')")
@@ -68,6 +71,11 @@ do_one_comparison <- function(
     })
     if (is.null(control_obj)) {
         print("          Skip (not enough cells in control)")
+        add_report(
+            list(kind = "error", content = "Not enough cells in control"),
+            h1 = groupname,
+            h2 = compname
+        )
         return (NULL)
     }
     exprs_case = GetAssayData(case_obj)
@@ -77,6 +85,11 @@ do_one_comparison <- function(
     dir.create(odir, showWarnings = FALSE)
     if (ncol(exprs_case) < 3 || ncol(exprs_control) < 3) {
         print("          Skip (not enough cells)")
+        add_report(
+            list(kind = "error", content = "Not enough cells"),
+            h1 = groupname,
+            h2 = compname
+        )
         return (NULL)
     }
     if (fgsea) {
@@ -95,6 +108,12 @@ do_one_comparison <- function(
             outdir = odir,
             envs = list(nproc = 1)
         )
+
+        add_report(
+            list(kind = "fgsea", dir = odir),
+            h1 = groupname,
+            h2 = compname
+        )
     } else {
         runGSEA(
             cbind(exprs_case, exprs_control),
@@ -114,7 +133,7 @@ do_one_group <- function(group) {
     )
     obj = eval(parse(text = group_code))
     groupname = paste0(grouping_prefix, group)
-    groupdir = file.path(outdir, groupname)
+    groupdir = file.path(outdir, slugify(groupname, tolower = FALSE))
     dir.create(groupdir, showWarnings = FALSE)
 
     for (i in seq_along(subsetting_comparison)) {
@@ -132,7 +151,8 @@ do_one_group <- function(group) {
                     sci[[compname]][2],
                     groupdir,
                     subsetting_cols[i],
-                    subsetting_prefix[i]
+                    subsetting_prefix[i],
+                    groupname
                 )
             }
         )
@@ -148,3 +168,5 @@ if (ncores == 1) {
         stop("mclapply error")
     }
 }
+
+save_report(joboutdir)

biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R

@@ -296,6 +296,7 @@ do_one_subset <- function(s, subset_col, subset_prefix) {
                 size = 1,
                 color = "black"
             )',
+            "scale_fill_biopipen()",
             "theme_prism(axis_text_angle = 90)"
         ),
         devpars = vio_devpars,

biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R

@@ -1,3 +1,4 @@
+source("{{biopipen_dir}}/utils/misc.R")
 source("{{biopipen_dir}}/utils/gsea.R")
 source("{{biopipen_dir}}/utils/plot.R")
 
@@ -7,9 +8,11 @@ library(ggprism)
 library(Matrix)
 library(sparseMatrixStats)
 library(Seurat)
+library(slugify)
 
 sobjfile <- {{ in.sobjfile | r }}
 outdir <- {{ out.outdir | r }}
+joboutdir <- {{ job.outdir | r }}
 gmtfile <- {{ envs.gmtfile | r }}
 select_pcs <- {{ envs.select_pcs | r }}
 ncores <- {{ envs.ncores | r }}
@@ -43,12 +46,12 @@ metabolics <- unique(as.vector(unname(unlist(pathways))))
 sobj <- readRDS(sobjfile)
 
 do_one_subset <- function(s, subset_col, subset_prefix) {
-    print(paste0("  Handling subset value: ", s, " ..."))
+    log_info(paste0("  Handling subset value: ", s, " ..."))
     if (is.null(s)) {
         subset_dir = file.path(outdir, "ALL")
         subset_obj = sobj
     } else {
-        subset_dir = file.path(outdir, paste0(subset_prefix, s))
+        subset_dir = file.path(outdir, slugify(paste0(subset_prefix, s), tolower = FALSE))
         subset_code = paste0("subset(sobj, subset = ", subset_col, " == '", s, "')")
         subset_obj = eval(parse(text = subset_code))
     }
@@ -214,10 +217,16 @@ do_one_subset <- function(s, subset_col, subset_prefix) {
         )
 
     ggsave(file.path(subset_dir, "PC_variance_plot.pdf"), p, device = "pdf", useDingbats = FALSE)
+
+    add_report(
+        list(kind = "descr", content = "Metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities"),
+        list(kind = "image", src = bubblefile),
+        h1 = ifelse(is.null(s), "Metabolic pathway heterogeneity", paste0(subset_prefix, s))
+    )
 }
 
 do_one_subset_col <- function(subset_col, subset_prefix) {
-    print(paste0("- Handling subset column: ", subset_col, " ..."))
+    log_info(paste0("- Handling subset column: ", subset_col, " ..."))
     if (is.null(subset_col)) {
         do_one_subset(NULL, subset_col = NULL, subset_prefix = NULL)
     }
@@ -240,3 +249,5 @@ if (is.null(subsetting_cols)) {
         do_one_subset_col(subsetting_cols[i], subsetting_prefix[i])
     }
 }
+
+save_report(joboutdir)

biopipen/scripts/tcr/Attach2Seurat.R

@@ -11,6 +11,7 @@ immfile = {{in.immfile | r}}
 sobjfile = {{in.sobjfile | r}}
 outfile = {{out.outfile | r}}
 metacols = {{envs.metacols | r}}
+prefix = {{envs.prefix | r}}
 
 immdata = readRDS(immfile)
 sobj = readRDS(sobjfile)
@@ -31,7 +32,7 @@ metadf = do_call(rbind, lapply(seq_len(nrow(immdata$meta)), function(i) {
 
     cldata %>%
         separate_rows(Barcode, sep=";") %>%
-        mutate(Barcode = glue("{{envs.prefix}}{Barcode}"))
+        mutate(Barcode = glue(paste0(prefix, "{Barcode}")))
 
 }))