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Adding support for Snakemake (XAMPPRocky#1045)
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# 67 lines 50 code 4 comments 13 blanks | ||
""" | ||
A sample Snakefile for testing line counting | ||
""" | ||
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SAMPLES = ["A", "B"] | ||
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# This is a | ||
# multiline | ||
# comment | ||
rule all: | ||
input: | ||
"plots/quals.svg" | ||
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'''Sometimes even some | ||
comments in single quote | ||
fences.''' | ||
rule bwa_map: | ||
input: | ||
"data/genome.fa", # Inline comments are also supported | ||
"data/samples/{sample}.fastq" | ||
output: | ||
"mapped_reads/{sample}.bam" | ||
shell: | ||
"bwa mem {input} | samtools view -Sb - > {output}" | ||
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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}" | ||
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rule samtools_index: | ||
input: | ||
"sorted_reads/{sample}.bam" | ||
output: | ||
"sorted_reads/{sample}.bam.bai" | ||
shell: | ||
"samtools index {input}" | ||
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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: | ||
"bcftools mpileup -f {input.fa} {input.bam} | " | ||
"bcftools call -mv - > {output}" | ||
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rule plot_quals: | ||
input: | ||
"calls/all.vcf" | ||
output: | ||
"plots/quals.svg" | ||
script: | ||
"scripts/plot-quals.py" |