diff --git a/project/config/config.yaml b/project/config/config.yaml index 3bcaa12952e9dc45a297cc528f4fa00da4458074..9d229a0f580ba04b94a0159e40e32d36eb8f63f4 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 a0b3d1f9e3b49ed2f6f88af0be203baa4bf66787..51a51673ffa7da1633dc0daface1c96b055f46fe 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