Update Snakefile_step2_single

BIGslu · Jun 26, 2024 · bbf32d4 · bbf32d4
1 parent 03051a6
commit bbf32d4
Showing 1 changed file with 2 additions and 3 deletions.
diff --git a/Snakefile_step2_single b/Snakefile_step2_single
@@ -38,14 +38,13 @@ rule adapterremoval:
     params:
         trim5p = config["trim5p"],
         trimAdapt = config["trimAdapt"],
-        adapter1 = config["adapter1"],
-        adapter2 = config["adapter2"]
+        adapter1 = config["adapter1"]
     threads: config["threads"] * 0.1
     message: "Adapter removal & quality filtering"
 
     run: 
         if params.trimAdapt == True:
-            shell("AdapterRemoval --file1 {input.R1} --output1 {output.R1} --singleton {output.single} --discarded {output.discard} --settings {output.set} --threads {threads} --gzip --maxns 1 --minlength 15 --trimqualities --minquality 30 --trim5p {params.trim5p} --adapter1 {params.adapter1} --adapter2 {params.adapter2}")
+            shell("AdapterRemoval --file1 {input.R1} --output1 {output.R1} --singleton {output.single} --discarded {output.discard} --settings {output.set} --threads {threads} --gzip --maxns 1 --minlength 15 --trimqualities --minquality 30 --trim5p {params.trim5p} --adapter1 {params.adapter1}")
         if params.trimAdapt == False:
             shell("AdapterRemoval --file1 {input.R1} --output1 {output.R1} --singleton {output.single} --discarded {output.discard} --settings {output.set} --threads {threads} --gzip --maxns 1 --minlength 15 --trimqualities --minquality 30 --trim5p {params.trim5p}")
         if params.trimAdapt != True and params.trimAdapt != False: