diff --git a/workflow/rules/1.1_fastq_processing.smk b/workflow/rules/1.1_fastq_processing.smk index 5c4f46c..35024b1 100644 --- a/workflow/rules/1.1_fastq_processing.smk +++ b/workflow/rules/1.1_fastq_processing.smk @@ -170,8 +170,9 @@ rule fastp_historical: "docker://quay.io/biocontainers/fastp:0.22.0--h2e03b76_0" shell: """ - fastp -i {input.R1} -I {input.R2} -p -c --merge --merged_out={output.merged} -o {output.R1_un} -O {output.R2_un} \ - -h {output.html} -j {output.json} -R '{params.report}' -w {threads} -l {params.readlength} 2> {log} + fastp -i {input.R1} -I {input.R2} -p -c --merge --overlap_len_require 15 --overlap_diff_limit 1 \ + --merged_out={output.merged} -o {output.R1_un} -O {output.R2_un} -h {output.html} -j {output.json} \ + -R '{params.report}' -w {threads} -l {params.readlength} 2> {log} """