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https://github.com/XAMPPRocky/tokei
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68 lines
1.3 KiB
Plaintext
68 lines
1.3 KiB
Plaintext
# 67 lines 50 code 4 comments 13 blanks
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"""
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A sample Snakefile for testing line counting
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"""
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SAMPLES = ["A", "B"]
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# This is a
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# multiline
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# comment
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rule all:
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input:
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"plots/quals.svg"
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'''Sometimes even some
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comments in single quote
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fences.'''
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rule bwa_map:
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input:
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"data/genome.fa", # Inline comments are also supported
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"data/samples/{sample}.fastq"
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output:
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"mapped_reads/{sample}.bam"
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shell:
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"bwa mem {input} | samtools view -Sb - > {output}"
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rule samtools_sort:
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input:
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"mapped_reads/{sample}.bam"
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output:
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"sorted_reads/{sample}.bam"
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shell:
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"samtools sort -T sorted_reads/{wildcards.sample} "
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"-O bam {input} > {output}"
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rule samtools_index:
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input:
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"sorted_reads/{sample}.bam"
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output:
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"sorted_reads/{sample}.bam.bai"
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shell:
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"samtools index {input}"
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rule bcftools_call:
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input:
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fa="data/genome.fa",
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bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
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output:
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"calls/all.vcf"
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shell:
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"bcftools mpileup -f {input.fa} {input.bam} | "
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"bcftools call -mv - > {output}"
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rule plot_quals:
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input:
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"calls/all.vcf"
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output:
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"plots/quals.svg"
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script:
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"scripts/plot-quals.py"
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