基于Snakemake的生信分析分析流程设计原则

约定大于配置（Convention over configuration）

config文件的准备

• config.yaml
• contrast.tsv
• metadata.tsv
• samples.tsv
• multiqc.yaml

samples.tsv

metadata.tsv

contrast.tsv

rule make_b_files:
	input:
		bam=expand(
            "results/hisat2/{sample.sample_name}/hisat2.bam",
            sample=samples.itertuples(),
        ),
		input1 = "results/MASTS/{group}/{condition1}.txt"
	output:
		b1 = "results/MASTS/{group}/{condition1}-{condition2}.txt"
		# b1 = "results/MASTS/{group}/{condition1}-{condition2}.txt"

	params:
		file1 = lambda w, input:[cond1_bam for cond1_bam in input.bam if w.condition1 in cond1_bam], # if cond1_bam.startswith("pass2/"+CONDITION1)
		file2 = lambda w, input:[cond2_bam for cond2_bam in input.bam if w.condition1 in cond2_bam]
	run:
		with open(output.b1,'w') as file1:
			file1.write(",".join(params.file1))

		# with open(output.b2,'w') as file2:
		# 	file2.write(",".join(params.file2))