有谁能告诉我在蛇形游戏官方教程中{sample}
和{wildcard.sample}
的区别,如下所示?
它们都等于“A”还是“B”?
我想知道什么时候使用{sample}
和{wildcard.sample}
。
谢谢
SAMPLES = ["A", "B"]
rule all:
input:
"plots/quals.svg"
rule bwa_map:
input:
"data/genome.fa",
"data/samples/{sample}.fastq"
output:
"mapped_reads/{sample}.bam"
shell:
"bwa mem {input} | samtools view -Sb - > {output}"
rule samtools_sort:
input:
"mapped_reads/{sample}.bam"
output:
"sorted_reads/{sample}.bam"
shell:
"samtools sort -T sorted_reads/{wildcards.sample} "
"-O bam {input} > {output}"
rule samtools_index:
input:
"sorted_reads/{sample}.bam"
output:
"sorted_reads/{sample}.bam.bai"
shell:
"samtools index {input}"
rule bcftools_call:
input:
fa="data/genome.fa",
bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
output:
"calls/all.vcf"
shell:
"samtools mpileup -g -f {input.fa} {input.bam} | "
"bcftools call -mv - > {output}"
rule plot_quals:
input:
"calls/all.vcf"
output:
"plots/quals.svg"
script:
"scripts/plot-quals.py"
{sample}用于“输入”或“输出”,而{wildcard.sample}用于“shell”,因为只有{wildcard.sample}检索实际的样例名称并传输到shell,shell中的命令才会运行。我想
相关问题 更多 >
编程相关推荐