From f6b702c2d2ecda12ef53fbcf228f351ac88776d1 Mon Sep 17 00:00:00 2001 From: Kimberly Dill-McFarland <21342185+kdillmcfarland@users.noreply.github.com> Date: Wed, 26 Jun 2024 13:19:37 -0700 Subject: [PATCH] Update Snakefile_step2_single Rm singleton output for single read AdapterRemoval --- Snakefile_step2_single | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/Snakefile_step2_single b/Snakefile_step2_single index e4f1c29..69a08d1 100644 --- a/Snakefile_step2_single +++ b/Snakefile_step2_single @@ -32,7 +32,6 @@ rule adapterremoval: R1 = lambda wildcards: config["SampleList"][wildcards.sample]["R1"] output: R1 = "result/1_trim/{sample}_R1_trim.fastq.gz", - single = "result/1_trim/{sample}_singleton.truncated.gz", discard = "result/1_trim/{sample}.settings", set = "result/1_trim/{sample}_discarded.gz" params: @@ -44,9 +43,9 @@ rule adapterremoval: 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}") + shell("AdapterRemoval --file1 {input.R1} --output1 {output.R1} --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}") + shell("AdapterRemoval --file1 {input.R1} --output1 {output.R1} --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: print("Error: Config trimAdapt parameter must be set to True or False.")