https://bioinformaticsonline.com/snippets/view/43590/rules-to-run-fastp-snakemake? https://bioinformaticsonline.com/snippets/view/43590/rules-to-run-fastp-snakemake Tue, 16 Nov 2021 01:03:22 -0600 https://bioinformaticsonline.com/snippets/view/43590/rules-to-run-fastp-snakemake rule fastp: input: fwd=INPUT + "/{sample}-read_1.fq", rev=INPUT + "/{sample}-read_2.fq" output: fwd=RESULTS + "/fastq_trimmed/{sample}.1.trimmed.fastq", rev=RESULTS + "/fastq_trimmed/{sample}.2.trimmed.fastq", html=RESULTS + "/fastq_trimmed/{sample}.html", json=RESULTS + "/fastq_trimmed/{sample}.json" threads: 5 log: RESULTS + "/logs/fastp/{sample}.preprocess.log" shell: "fastp --in1 {input.fwd} --in2 {input.rev} " "--out1 {output.fwd} --out2 {output.rev} --thread {threads} --cut_tail --html {output.html} --json {output.json} 2> {log}"]]> Abhi