nextflow入门（一) - un

生信分析流工具常见流派snakemake、wdl、cwl、nextflow,甚至还有make流，在snakemake和nextflow之间反复横跳后，发现最好两个都要会。

官方网站: https://www.nextflow.io/docs/latest/index.html

安装

依赖java环境，当前nextflow版本为25.10.2

curl -s https://get.nextflow.io | bash
chmod +x nextflow

测试文件构建

在data目录下创建20个双端测序空文件备用

seq 1 20|xargs -I {}  touch sample_{}_1.fq
seq 1 20|xargs -I {}  touch sample_{}_2.fq

编写一个测试例子

#!/usr/bin/env nextflownextflow.enable.dsl = 2params.read_path = "${workflow.projectDir}/data"
params.outdir = "${workflow.projectDir}/result"
params.pattern = "*_{1,2}.fq"process chd {publishDir  params.outdir, mode: 'link'input:tuple val(sample_id), path(reads)output:path "${sample_id}_info.txt", emit: sample_infoscript:"""echo  "sample_id: $sample_id, seq_file: ${reads[0]}:\t:${reads[1]}" > ${sample_id}_info.txt"""// 三重单引号内变量获取方式 !{variable}// ''' echo "sample_id: !{sample_id}, seq_file: !{reads}"  '''
}process cats {publishDir params.outdir, mode: 'link'cache 'lenient' // 避免重复运行input:path(sample_files)output:path "merged.txt"script:"""for file in ${sample_files}; docat \$file >> "merged.txt"done"""
}workflow {println "workdir: ${workflow.projectDir}"ch_fq = channel.fromFilePairs("${params.read_path}/${params.pattern}", flat: false, checkIfExists: true)// 显式声明参数名（比如sample_data），替换隐式的itch_fq.view { sample_data ->  "raw ctx: sm=${sample_data[0]}, fq1 = ${sample_data[1][0]}, fq2= ${sample_data[1][1]}" }chd_out = chd(ch_fq)res1 = chd_out.sample_info.collect()cats(res1)
}