biopipen 0.29.1__py3-none-any.whl → 0.30.0__py3-none-any.whl

biopipen/scripts/scrna/SeuratSubClustering.R

@@ -1,5 +1,5 @@
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/caching.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "caching.R" | source_r }}
 
 library(Seurat)
 library(future)
@@ -8,7 +8,6 @@ library(tidyr)
 library(dplyr)
 library(tidyseurat)
 library(digest)
-library(clustree)
 
 set.seed(8525)
 
@@ -39,13 +38,13 @@ plan(strategy = "multicore", workers = envs$ncores)
             parts <- trimws(unlist(strsplit(res, ",")))
             for (part in parts) {
                 if (grepl(":", part)) {
-                    parts <- trimws(unlist(strsplit(part, ":")))
-                    if (length(parts) == 2) { parts <- c(parts, 0.1) }
-                    if (length(parts) != 3) {
+                    ps <- trimws(unlist(strsplit(part, ":")))
+                    if (length(ps) == 2) { ps <- c(ps, 0.1) }
+                    if (length(ps) != 3) {
                         stop("Invalid resolution format: {part}. Expected 2 or 3 parts separated by ':' for a range.")
                     }
-                    parts <- as.numeric(parts)
-                    expanded_res <- c(expanded_res, seq(parts[1], parts[2], by = parts[3]))
+                    ps <- as.numeric(ps)
+                    expanded_res <- c(expanded_res, seq(ps[1], ps[2], by = ps[3]))
                 } else {
                     expanded_res <- c(expanded_res, as.numeric(part))
                 }
@@ -53,7 +52,7 @@ plan(strategy = "multicore", workers = envs$ncores)
         }
     }
     # keep the last resolution at last
-    rev(unique(rev(expanded_res)))
+    rev(unique(rev(round(expanded_res, 2))))
 }
 
 # recode clusters from 0, 1, 2, ... to s1, s2, s3, ...
@@ -98,8 +97,7 @@ for (key in names(envs$cases)) {
             subset = envs$subset,
             RunUMAP = envs$RunUMAP,
             FindNeighbors = envs$FindNeighbors,
-            FindClusters = envs$FindClusters,
-            clustree_devpars = envs$clustree_devpars
+            FindClusters = envs$FindClusters
         ),
         case
     )
@@ -169,49 +167,36 @@ for (key in names(envs$cases)) {
 
     case$FindClusters$random.seed <- case$FindClusters$random.seed %||% 8525
     resolution <- case$FindClusters$resolution <- .expand_resolution(case$FindClusters$resolution %||% 0.8)
-    cached <- get_cached(case$FindClusters, "FindClusters", cache_dir)
+    cached <- get_cached(case$FindClusters, "SubClustering", cache_dir)
     if (is.null(cached$data)) {
         log_info("- Running FindClusters at resolution: {paste(resolution, collapse = ',')} ...")
         case$FindClusters$object <- sobj
-        # avoid overwriting the previous clustering results (as they have the same graph name
+        case$FindClusters$cluster.name <- paste0(key, ".", resolution)
+        # use sobj1 to avoid overwriting the previous clustering results (as they have the same graph name
         sobj1 <- do_call(FindClusters, case$FindClusters)
-        graph_name <- case$FindClusters$graph.name %||% paste0(DefaultAssay(sobj), "_snn_res.")
-        for (res in resolution) {
-            cluster_name <- paste0(graph_name, res)
-            new_cluster_name <- paste0(key, ".", res)
-            sobj1@meta.data[[new_cluster_name]] <- .recode_clusters(sobj1@meta.data[[cluster_name]])
-        }
         sobj1@meta.data[[key]] <- .recode_clusters(sobj1@meta.data$seurat_clusters)
-        keys <- sapply(resolution, function(res) paste0(key, ".", res))
-        keys <- c(keys, key)
-        cached$data <- sobj1@meta.data[, keys, drop = FALSE]
-        save_to_cache(cached, "FindClusters", cache_dir)
+        for (clname in case$FindClusters$cluster.name) {
+            sobj1@meta.data[[clname]] <- .recode_clusters(sobj1@meta.data[[clname]])
+        }
+        cached$data <- list(
+            clusters = sobj1@meta.data[, c(case$FindClusters$cluster.name, key), drop = FALSE],
+            command = sobj1@commands$FindClusters
+        )
+        save_to_cache(cached, "SubClustering", cache_dir)
         rm(sobj1)
     } else {
         log_info("- Using cached FindClusters at resolution: {paste(resolution, collapse = ',')} ...")
     }
 
-    ident_table <- table(cached$data[[key]])
-    log_info("  Found {length(ident_table)} clusters")
+    ident_table <- table(cached$data$clusters[[key]])
+    log_info("  Found {length(ident_table)} clusters at resolution: {resolution[length(resolution)]}")
     print(ident_table)
     cat("\n")
 
-    if (length(resolution) > 1) {
-        log_info("- Plotting clustree ...")
-        png(
-            file.path(joboutdir, paste0(key, ".clustree.png")),
-            res = case$clustree_devpars$res,
-            width = case$clustree_devpars$width,
-            height = case$clustree_devpars$height
-        )
-        p <- clustree(cached$data, prefix = paste0(key, "."))
-        print(p)
-        dev.off()
-    }
-
     log_info("- Updating meta.data with subclusters...")
-    srtobj <- AddMetaData(srtobj, metadata = cached$data)
+    srtobj <- AddMetaData(srtobj, metadata = cached$data$clusters)
     srtobj[[paste0("sub_umap_", key)]] <- reduc
+    srtobj@commands[[paste0("FindClusters.", key)]] <- cached$data$command
 }
 
 log_info("Saving results ...")

biopipen/scripts/scrna/TopExpressingGenes.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/misc.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 
 library(Seurat)
 library(tibble)

biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R

@@ -1,5 +1,5 @@
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/gsea.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "gsea.R" | source_r }}
 
 library(parallel)
 library(Seurat)
@@ -139,8 +139,11 @@ do_one_subset <- function(s, subset_col, subset_prefix) {
     if (any(unlist(lapply(x, class)) == "try-error")) {
         stop("mclapply error")
     }
-
-    for (r in x) { do.call(add_report, r) }
+    for (r in x) {
+        if (!is.null(r)) {
+            do.call(add_report, r)
+        }
+    }
 }
 
 do_one_subset_col <- function(subset_col, subset_prefix) {

biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R

@@ -1,5 +1,5 @@
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/gsea.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "gsea.R" | source_r }}
 
 library(parallel)
 library(scater)
@@ -184,6 +184,10 @@ if (ncores == 1) {
     }
 }
 report = unlist(x, recursive = FALSE)
-for (r in report) { do.call(add_report, r) }
+for (r in report) {
+    if (!is.null(r)) {
+        do.call(add_report, r)
+    }
+}
 
 save_report(joboutdir)

biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R

@@ -1,6 +1,6 @@
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/gsea.R")
-source("{{biopipen_dir}}/utils/plot.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "gsea.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 
 library(scater)
 library(reshape2)

biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R

@@ -1,6 +1,6 @@
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/gsea.R")
-source("{{biopipen_dir}}/utils/plot.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "gsea.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 
 library(gtools)
 library(parallel)

biopipen/scripts/snp/MatrixEQTL.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/misc.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 library(rlang)
 library(rtracklayer)
 library(MatrixEQTL)

biopipen/scripts/snp/PlinkCallRate.R

@@ -1,5 +1,5 @@
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/plot.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 library(ggprism)
 theme_set(theme_prism())
 

biopipen/scripts/snp/PlinkFreq.R

@@ -1,5 +1,5 @@
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/plot.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 library(rlang)
 library(ggprism)
 theme_set(theme_prism())

biopipen/scripts/snp/PlinkHWE.R

@@ -1,5 +1,5 @@
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/plot.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 library(ggprism)
 theme_set(theme_prism())
 

biopipen/scripts/snp/PlinkHet.R

@@ -1,5 +1,5 @@
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/plot.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 library(ggprism)
 theme_set(theme_prism())
 

biopipen/scripts/snp/PlinkIBD.R

@@ -1,5 +1,5 @@
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/plot.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 suppressPackageStartupMessages({
     library(dplyr)
     library(tidyr)

biopipen/scripts/stats/ChowTest.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/misc.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 
 library(rlang)
 library(dplyr)

biopipen/scripts/stats/DiffCoexpr.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/misc.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 library(dcanr)
 library(scuttle)
 library(doRNG)

biopipen/scripts/stats/LiquidAssoc.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/misc.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 
 library(rlang)
 library(dplyr)

biopipen/scripts/stats/Mediation.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/misc.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 
 library(rlang)
 library(parallel)
@@ -35,9 +35,20 @@ if (!is.null(fmlfile)) {
 
 args <- args %||% list()
 
-medanalysis = function(casename) {
+medanalysis <- function(i, total) {
+    casename <- names(cases)[i]
     case <- cases[[casename]]
-    log_info("- Case:", casename)
+    if (total < 50) {
+        log_info("- Case: ", casename)
+    } else if (total < 500) {
+        if (i %% 10 == 0) {
+            log_info("- Processing case {i}/{total} ...")
+        }
+    } else {
+        if (i %% 100 == 0) {
+            log_info("- Processing case {i}/{total} ...")
+        }
+    }
     M <- case$M
     Y <- case$Y
     X <- case$X
@@ -55,17 +66,19 @@ medanalysis = function(casename) {
         fmly <- update.formula(fmly, cov_fml)
     }
 
+    data <- indata[, c(M, X, Y, covs), drop = FALSE]
+    data <- data[complete.cases(data), , drop = FALSE]
     margs <- args
-    args$sims <- sims
-    args$model.m <- modelm(fmlm, data = indata)
-    args$model.y <- modely(fmly, data = indata)
-    args$treat <- X
-    args$mediator <- M
-    args$outcome <- Y
+    margs$sims <- sims
+    margs$model.m <- modelm(fmlm, data = data)
+    margs$model.y <- modely(fmly, data = data)
+    margs$treat <- X
+    margs$mediator <- M
+    margs$outcome <- Y
     if (!is.null(covs)) {
-        args$covariates <- indata[, covs, drop = FALSE]
+        margs$covariates <- data[, covs, drop = FALSE]
     }
-    med <- do_call(mediate, args)
+    med <- do_call(mediate, margs)
     if (is.na(med$d1.p) || is.na(med$n1)) {
         NULL
     } else {
@@ -85,7 +98,8 @@ medanalysis = function(casename) {
     }
 }
 
-out <- do_call(rbind, mclapply(names(cases), medanalysis, mc.cores = ncores))
+total <- length(cases)
+out <- do_call(rbind, mclapply(1:total, medanalysis, total = total, mc.cores = ncores))
 
 if (padj != "none") {
     out$Padj <- p.adjust(out$Pval, method = padj)

biopipen/scripts/stats/MetaPvalue.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/misc.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 
 library(metap)
 library(rlang)
@@ -106,6 +106,9 @@ if (length(infiles) == 1 && padj == "none") {
         } else if (length(ps) == 1 && keep_single) {
             metaps <- c(metaps, ps)
             ns <- c(ns, 1)
+        } else if (any(ps == 0)) {
+            metaps <- c(metaps, 0)
+            ns <- c(ns, length(ps))
         } else {
             metaps <- c(metaps, do.call(method, list(ps))$p)
             ns <- c(ns, length(ps))

biopipen/scripts/stats/MetaPvalue1.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/misc.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 
 library(metap)
 library(rlang)
@@ -50,6 +50,9 @@ for (ps in outdata$.pvals) {
     } else if (length(ps) == 1 && keep_single) {
         metaps <- c(metaps, ps)
         ns <- c(ns, 1)
+    } else if (any(ps == 0)) {
+        metaps <- c(metaps, 0)
+        ns <- c(ns, length(ps))
     } else {
         metaps <- c(metaps, do.call(method, list(ps))$p)
         ns <- c(ns, length(ps))

biopipen/scripts/tcr/Attach2Seurat.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/misc.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 
 library(Seurat)
 library(immunarch)

biopipen/scripts/tcr/CDR3AAPhyschem.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/misc.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 library(dplyr)
 library(tidyr)
 library(tibble)

biopipen/scripts/tcr/CloneResidency.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/misc.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 
 library(rlang)
 library(dplyr)
@@ -414,7 +414,7 @@ handle_subject <- function(i, subjects, casename, case) {
         mutate(across(everything(), as.character)) %>%
         paste(collapse = "-")
 
-    log_info("  Handling {subject} ({i}/{nrow(subjects)}) ...")
+    log_info("  Handling {i}/{nrow(subjects)}: {subject} ...")
 
     if (!is.null(case$subset)) {
         counts <- cldata %>% filter(!!parse_expr(case$subset))

biopipen/scripts/tcr/CloneSizeQQPlot.R

@@ -1,5 +1,5 @@
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/plot.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 
 library(dplyr)
 library(tidyr)

biopipen/scripts/tcr/Immunarch-basic.R

@@ -5,10 +5,6 @@ log_info("")
 log_info("# Basic analysis")
 log_info("-----------------------------------")
 
-volumes = {{envs.volumes | r}}
-lens = {{envs.lens | r}}
-counts = {{envs.counts | r}}
-
 # Fill up cases
 fill_up_cases_basic = function(config) {
     log_debug("Filling up cases ...")

biopipen/scripts/tcr/Immunarch-clonality.R

@@ -5,10 +5,6 @@ log_info("")
 log_info("# Clonality analysis")
 log_info("-----------------------------------")
 
-top_clones = {{envs.top_clones | r}}
-rare_clones = {{envs.rare_clones | r}}
-hom_clones = {{envs.hom_clones | r}}
-
 # Fill up cases
 fill_up_cases_clonality = function(config) {
     cases = config$cases

biopipen/scripts/tcr/Immunarch-diversity.R

@@ -1,32 +1,10 @@
-# Diversity estimation
-source("{{biopipen_dir}}/scripts/tcr/immunarch-patched.R")
+
 # https://immunarch.com/articles/web_only/v6_diversity.html
 
 log_info("")
 log_info("# Diversity estimation")
 log_info("-----------------------------------")
 
-# Other variables are loaded in the parent template
-# immdata is already loaded, meta is mutated
-div_method = {{envs.divs.method | default: "gini" | r}}
-div_by = {{envs.divs.by | default: None | r}}
-div_plot_type = {{envs.divs.plot_type | default: "bar" | r}}
-div_order = {{envs.divs.order | default: [] | r}}
-div_args = {{envs.divs.args | default: {} | r: todot="-"}}
-div_test = {{envs.divs.test | default: None | r}}
-div_cases = {{envs.divs.cases | default: {} | r: todot="-"}}
-div_devpars = {{envs.divs.devpars | default: None | r}}
-div_separate_by = {{envs.divs.separate_by | default: None | r}}
-div_split_by = {{envs.divs.split_by | default: None | r}}
-div_split_order = {{envs.divs.split_order | default: None | r}}
-div_align_x = {{envs.divs.align_x | default: False | r}}
-div_align_y = {{envs.divs.align_y | default: False | r}}
-div_subset = {{envs.divs.subset | default: None | r}}
-div_log = {{envs.divs.log | default: False | r}}
-div_ncol = {{envs.divs.ncol | default: 2 | r}}
-div_ymin = {{envs.divs.ymin | default: None | r}}
-div_ymax = {{envs.divs.ymax | default: None | r}}
-
 div_test = div_test %||% list(method = "none", padjust = "none")
 div_devpars = div_devpars %||% list(res = 100, width = 800, height = 800)
 
@@ -77,7 +55,7 @@ update_case = function(case, name) {
     if (!is.null(case$args) && length(case$args) > 0) {
         names(case$args) = paste0(".", names(case$args))
     }
-    if (!is.null(case$test) && case$test != "none" && (is.null(case$by) || length(case$by) == 0)) {
+    if (!is.null(case$test) && case$test$method != "none" && (is.null(case$by) || length(case$by) == 0)) {
         stop("For diversity estimation, `test` is only supported when `by` is specified")
     }
     # Just ignore them for rarefraction

biopipen/scripts/tcr/Immunarch-geneusage.R

@@ -5,8 +5,6 @@ log_info("")
 log_info("# Gene usage analysis")
 log_info("-----------------------------------")
 
-gene_usages = {{ envs.gene_usages | r: todot="-" }}
-
 # Fill up cases
 log_info("Filling up cases ...")
 cases = gene_usages$cases

biopipen/scripts/tcr/Immunarch-kmer.R

@@ -5,8 +5,6 @@ log_info("")
 log_info("# K-mer analysis")
 log_info("-----------------------------------")
 
-kmers = {{ envs.kmers | r: todot="-" }}
-
 # Fill up cases
 log_info("Filling up cases ...")
 cases = kmers$cases

biopipen/scripts/tcr/Immunarch-overlap.R

@@ -5,8 +5,6 @@ log_info("")
 log_info("# Overlap analysis")
 log_info("-----------------------------------")
 
-overlaps = {{ envs.overlaps | r: todot="-" }}
-
 # Fill up cases
 cases = overlaps$cases
 if (is.null(cases) || length(cases) == 0) {

biopipen/scripts/tcr/Immunarch-spectratyping.R

@@ -5,8 +5,6 @@ log_info("")
 log_info("# Spectratyping analysis")
 log_info("-----------------------------------")
 
-spects = {{ envs.spects | r }}
-
 # Fill up cases
 log_info("Filling up cases ...")
 if (is.null(spects$cases) || length(spects$cases) == 0) {

biopipen/scripts/tcr/Immunarch-tracking.R

@@ -2,8 +2,6 @@ log_info("")
 log_info("# Clonotype tracking")
 log_info("-----------------------------------")
 
-trackings = {{ envs.trackings | r }}
-
 log_info("Filling up cases ...")
 if (is.null(trackings$subjects)) {
     trackings$subjects = c()

biopipen/scripts/tcr/Immunarch-vjjunc.R

@@ -5,8 +5,6 @@ log_info("-----------------------------------")
 # Already required by immunarch
 library(circlize)
 
-vj_juncs <- {{envs.vj_junc | r}}
-
 log_info("Filling up cases ...")
 cases <- vj_juncs$cases
 if (is.null(cases) || length(cases) == 0) {

biopipen/scripts/tcr/Immunarch.R

@@ -1,5 +1,5 @@
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/single_cell.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
+{{ biopipen_dir | joinpaths: "utils", "single_cell.R" | source_r }}
 # Basic analysis and clonality
 # TODO: How about TRA chain?
 library(rlang)
@@ -65,46 +65,78 @@ n_samples = length(immdata$data)
 ##################
 # Basic analysis #
 ##################
-{% include biopipen_dir + "/scripts/tcr/Immunarch-basic.R" %}
+volumes = {{envs.volumes | r}}
+lens = {{envs.lens | r}}
+counts = {{envs.counts | r}}
+{{ biopipen_dir | joinpaths: "scripts", "tcr", "Immunarch-basic.R" | source_r }}
 
 ##################
 # Clonality      #
 ##################
-{% include biopipen_dir + "/scripts/tcr/Immunarch-clonality.R" %}
+top_clones = {{envs.top_clones | r}}
+rare_clones = {{envs.rare_clones | r}}
+hom_clones = {{envs.hom_clones | r}}
+{{ biopipen_dir | joinpaths: "scripts", "tcr", "Immunarch-clonality.R" | source_r }}
 
 ##################
 # Overlap        #
 ##################
-{% include biopipen_dir + "/scripts/tcr/Immunarch-overlap.R" %}
+overlaps = {{ envs.overlaps | r: todot="-" }}
+{{ biopipen_dir | joinpaths: "scripts", "tcr", "Immunarch-overlap.R" | source_r }}
 
 ##################
 # Gene usage     #
 ##################
-{% include biopipen_dir + "/scripts/tcr/Immunarch-geneusage.R" %}
+gene_usages = {{ envs.gene_usages | r: todot="-" }}
+{{ biopipen_dir | joinpaths: "scripts", "tcr", "Immunarch-geneusage.R" | source_r }}
 
 ##################
 # Spectratyping  #
 ##################
-{% include biopipen_dir + "/scripts/tcr/Immunarch-spectratyping.R" %}
+spects = {{ envs.spects | r }}
+{{ biopipen_dir | joinpaths: "scripts", "tcr", "Immunarch-spectratyping.R" | source_r }}
 
 ########################
 # Diversity estimation #
 ########################
-{% include biopipen_dir + "/scripts/tcr/Immunarch-diversity.R" %}
+div_method = {{envs.divs.method | default: "gini" | r}}
+div_by = {{envs.divs.by | default: None | r}}
+div_plot_type = {{envs.divs.plot_type | default: "bar" | r}}
+div_order = {{envs.divs.order | default: [] | r}}
+div_args = {{envs.divs.args | default: {} | r: todot="-"}}
+div_test = {{envs.divs.test | default: None | r}}
+div_cases = {{envs.divs.cases | default: {} | r: todot="-"}}
+div_devpars = {{envs.divs.devpars | default: None | r}}
+div_separate_by = {{envs.divs.separate_by | default: None | r}}
+div_split_by = {{envs.divs.split_by | default: None | r}}
+div_split_order = {{envs.divs.split_order | default: None | r}}
+div_align_x = {{envs.divs.align_x | default: False | r}}
+div_align_y = {{envs.divs.align_y | default: False | r}}
+div_subset = {{envs.divs.subset | default: None | r}}
+div_log = {{envs.divs.log | default: False | r}}
+div_ncol = {{envs.divs.ncol | default: 2 | r}}
+div_ymin = {{envs.divs.ymin | default: None | r}}
+div_ymax = {{envs.divs.ymax | default: None | r}}
+
+{{ biopipen_dir | joinpaths: "scripts", "tcr", "immunarch-patched.R" | source_r }}
+{{ biopipen_dir | joinpaths: "scripts", "tcr", "Immunarch-diversity.R" | source_r }}
 
 ######################
 # Clonotype tracking #
 ######################
-{% include biopipen_dir + "/scripts/tcr/Immunarch-tracking.R" %}
+trackings = {{ envs.trackings | r }}
+{{ biopipen_dir | joinpaths: "scripts", "tcr", "Immunarch-tracking.R" | source_r }}
 
 ######################
 # K-mer analysis     #
 ######################
-{% include biopipen_dir + "/scripts/tcr/Immunarch-kmer.R" %}
+kmers = {{ envs.kmers | r: todot="-" }}
+{{ biopipen_dir | joinpaths: "scripts", "tcr", "Immunarch-kmer.R" | source_r }}
 
 ######################
 # VJ junction        #
 ######################
-{% include biopipen_dir + "/scripts/tcr/Immunarch-vjjunc.R" %}
+vj_juncs <- {{envs.vj_junc | r}}
+{{ biopipen_dir | joinpaths: "scripts", "tcr", "Immunarch-vjjunc.R" | source_r }}
 
 save_report(joboutdir)

biopipen/scripts/tcr/ImmunarchFilter.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/misc.R")
+{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 
 library(dplyr)
 library(glue)