added fastp params #4

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"
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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"
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