From d377dd5514024245542d1c88c33596021a61f351 Mon Sep 17 00:00:00 2001
From: seehagec01 <seehagec01@mi.fu-berlin.de>
Date: Wed, 11 May 2022 14:48:01 +0200
Subject: [PATCH] added fastp params #4

---
 project/config/config.yaml       |  1 +
 project/workflow/rules/fastp.smk | 10 +---------
 2 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/project/config/config.yaml b/project/config/config.yaml
index 3bcaa12..9d229a0 100644
--- a/project/config/config.yaml
+++ b/project/config/config.yaml
@@ -8,3 +8,4 @@ viral_reference_alignment: "resources/reference/SARS-CoV-2.fasta"
 shiver_config_file: "config/shiver_config.sh"
 viral_sequencing_adapters: "resources/adapters/SARS-CoV-2.fasta"
 viral_sequencing_primers: "resources/primers/SARS-CoV-2.fasta"
+fastp_params: "--adapter_sequence TCTCGGTC --adapter_sequence_r2 GCGGACTT"
\ No newline at end of file
diff --git a/project/workflow/rules/fastp.smk b/project/workflow/rules/fastp.smk
index a0b3d1f..51a5167 100644
--- a/project/workflow/rules/fastp.smk
+++ b/project/workflow/rules/fastp.smk
@@ -3,13 +3,6 @@ rule fastp:
         sample=["Data/SARS-Cov-2/{sample}_1.fastq.gz", "Data/SARS-Cov-2/{sample}_2.fastq.gz"]
     output:
         trimmed=["results/fastp/trimmed/{sample}.1.fastq", "results/fastp/trimmed/{sample}.2.fastq"],
-        # Unpaired reads separately
-        #unpaired1="results/fastp/trimmed/{sample}.u1.fastq",
-        #unpaired2="results/fastp/trimmed/{sample}.u2.fastq",
-        # or in a single file
-        # unpaired="trimmed/{sample}.singletons.fastq",
-        #merged="results/fastp/trimmed/{sample}.merged.fastq",
-        #failed="results/fastp/trimmed/{sample}.failed.fastq",
         html="report/fastp/{sample}.html",
         json="report/fastp/{sample}.json"
     log:
@@ -17,8 +10,7 @@ rule fastp:
     conda:
         "../envs/yourenv.yaml"
     params:
-        # adapters="--adapter_sequence ACGGCTAGCTA --adapter_sequence_r2 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
-        #extra="--merge"
+        extra=config["fastp_params]
     threads: 4
     wrapper:
         "v1.3.2/bio/fastp"
\ No newline at end of file
-- 
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