From 4b799587ce56896d7c6052dc95b09fc16d62e6d7 Mon Sep 17 00:00:00 2001
From: Anne Bertolini <bertolini@nexus.ethz.ch>
Date: Tue, 10 Oct 2023 16:42:13 +0200
Subject: [PATCH] [FEAT] Add rule for dsb normalization of ADT counts

---
 workflow/rules/adt_dsb_normalization.smk | 36 ++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 workflow/rules/adt_dsb_normalization.smk

diff --git a/workflow/rules/adt_dsb_normalization.smk b/workflow/rules/adt_dsb_normalization.smk
new file mode 100644
index 0000000..ac567b4
--- /dev/null
+++ b/workflow/rules/adt_dsb_normalization.smk
@@ -0,0 +1,36 @@
+import os
+
+WORKDIR = os.getcwd()
+
+
+# Rule normalizing the ADT counts using R package "dsb"
+# Input is cellranger ADT output
+# Output is SCE object in RDS file
+rule dsb_normalize_adt:
+    input:
+        CellrangerADT="results/cellranger_adt/{sample}.matrix.mtx",
+    output:
+        normalized="results/dsb_normalize_adt/{sample}.dsb_normalize_adt.RDS",
+    conda:
+        "../envs/dsb_normalize_adt.yaml"
+    params:
+        adt_raw_dir=WORKDIR
+        + "/results/cellranger_adt/{sample}/outs/raw_feature_bc_matrix/",
+        adt_filtered_dir=WORKDIR
+        + "/results/cellranger_adt/{sample}/outs/filtered_feature_bc_matrix/",
+        outdir="results/dsb_normalize_adt/",
+        custom_script=workflow.source_path("../scripts/dsb_normalize_adt.R"),
+    threads: config["computingResources"]["threads"]["high"]
+    log:
+        "logs/dsb_normalize_adt/{sample}.log",
+    resources:
+        mem_mb=config["computingResources"]["mem_mb"]["high"],
+        runtime=config["computingResources"]["runtime"]["high"],
+    benchmark:
+        "results/dsb_normalize_adt/benchmark/{sample}.benchmark"
+    shell:
+        "Rscript {params.custom_script} "
+        "--adt_raw_dir {params.adt_raw_dir} "
+        "--adt_filtered_dir {params.adt_filtered_dir} "
+        "--outdir {params.outdir} "
+        "--sample {wildcards.sample} "