snakemake_examples/exercise0/Snakefile @ b4041cdc
| b4041cdc | c.toffano-nioche | samples=["P01325", "P01308"]
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| 1e5111ea | chloe.quignot | ||
rule targets:
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input:
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expand("fasta/{sample}.fasta", sample=samples),
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"fusionFasta/allSequences.fasta",
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"mafft/mafft_res.fasta",
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rule loadData:
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output:
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"fasta/{sample}.fasta",
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log:
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stdout = "logs/{sample}_wget.stdout",
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stderr = "logs/{sample}_wget.stderr",
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params:
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dirFasta = "fasta",
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threads: 1
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shell:
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"""
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wget --output-file {log.stderr} \
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--directory-prefix {params.dirFasta} \
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https://www.uniprot.org/uniprot/{wildcards.sample}.fasta > {log.stdout}
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"""
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rule fusionFasta:
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input:
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expand("fasta/{sample}.fasta", sample=samples),
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output:
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"fusionFasta/allSequences.fasta",
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log:
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"logs/fusionData.stderr",
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threads: 1
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shell:
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"""
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cat {input} > {output} 2> {log}
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"""
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rule mafft:
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input:
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rules.fusionFasta.output,
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output:
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"mafft/mafft_res.fasta",
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log:
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"logs/whichMafft.txt",
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threads: 1
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shell:
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"""
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mafft {input} > {output} 2> {log}
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"""
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