snakemake代码 [code]CASE_NAME = ["6dah-50-rep2"] READ_INDEX = ["1","2"] HISAT_INDEX = "/home/zhangyt/reference/SL2.50_index_hisat2/Solanum_lycopersicum.SL2.50.dna.genome.fa" CUFFLINKS_INDEX = "/home/zhangyt/reference/SL2.50_gff/Solanum_lycopersicum.SL2.50.37.chr.change_name.gff3" rule all: input: # expand("cutadapt.fastq/TI2-{case_name}-rep{rep_index}_R{read_index}_cutadapt.fq.gz",case_name=CASE_NAME, rep_index=REP_INDEX,read_index=READ_INDEX) expand("cutadapt.fastq/cutadapt_add2.fastq/TI2-{case_name}_R{read_index}_trim125.fq.gz",case_name=CASE_NAME, read_index=READ_INDEX), expand("bam/bam_add2/TI2-{case_name}_hisat2_sort.bam", case_name=CASE_NAME), expand("bam/bam_add2/TI2-{case_name}_hisat2_sort.bam.bai", case_name=CASE_NAME) rule cutadapt: input: "raw.fastq/raw_add2.fastq/TI2-{case_name}_R1.fastq.gz", "raw.fastq/raw_add2.fastq/TI2-{case_name}_R2.fastq.gz" output: "cutadapt.fastq/cutadapt_add2.fastq/TI2-{case_name}_R1_cutadapt.fq.gz", "cutadapt.fastq/cutadapt_add2.fastq/TI2-{case_name}_R2_cutadapt.fq.gz" log: "cutadapt.fastq/cutadapt_add2.fastq/TI2-{case_name}_cutadapt.log" shell: "cutadapt --times 1 -e 0.1 -O 3 -m 135 \ -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \ -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT \ -o {output[0]} -p {output[1]} {input[0]} {input[1]} > {log} 2>&1"[/code]log文件内容： [attach]9[/attach]