added rule for bandage

LiaOb21 · Apr 9, 2024 · 55e85b7 · 55e85b7
1 parent 66faa38
commit 55e85b7
Showing 1 changed file with 37 additions and 0 deletions.
diff --git a/workflow/rules/bandage.smk b/workflow/rules/bandage.smk
@@ -0,0 +1,37 @@
+rule bandage:
+    input:
+        "results/oatk/oatk.asm.mito.gfa"
+    output:
+        "results/bandage/mito.jpg"
+    threads: config["fastp"]["t"]
+    log:
+        "logs/bandage.log",
+    resources:
+        mem_mb=config['fastp']['mem_mb'],  # access memory from config
+    conda:
+        "../envs/bandage.yaml"
+    shell:
+        """
+        Bandage image {input} {output}
+        """
+
+
+rule bandage_pltd:
+    input:
+        mito_gfa = "results/oatk_pltd/oatk.asm.mito.gfa",
+        pltd_gfa = "results/oatk_pltd/oatk.asm.pltd.gfa"
+    output:
+        mito_out = "results/bandage_pltd/mito.jpg",
+        pltd_out = "results/bandage_pltd/pltd.jpg"
+    threads: config["fastp"]["t"]
+    log:
+        "logs/bandage.log",
+    resources:
+        mem_mb=config['fastp']['mem_mb'],  # access memory from config
+    conda:
+        "../envs/bandage.yaml"
+    shell:
+        """
+        Bandage image {input.mito_gfa} {output.mito_out}
+        Bandage image {input.pltd_gfa} {output.pltd_out}
+        """