Revision dc329d66
Added by Chloé QUIGNOT over 1 year ago
| exercise0_improved_after_1B/Snakefile | ||
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# Update 1: integrate Python skills within the SnakeFile using
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# the yaml module to read a samples.yaml file to import
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# your Uniprot ids as a list
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# NB: it's always a good idea to separate generalised
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# code and project-specific variable values
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import yaml
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with open('samples.yaml', 'r') as file
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content = yaml.safe_load(file)
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samples = content['samples']
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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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# Update 2: add params directive to specify the output directory
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# Update 3: add log directives to loadData, fusionFasta and mafft
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# rules to specify in which files standard output and
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# standard error are saved & integrate the necessary
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# wildcards within the shell directives
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rule loadData:
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output:
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"fasta/{sample}.fasta",
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params:
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dirFasta = "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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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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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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"fusionFasta/allSequences.fasta",
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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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shell:
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"""
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mafft {input} > {output} 2> {log}
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"""
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| exercise0_improved_after_1B/readme_runSnake.txt | ||
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Pour faire fonctionner le pipeline il faut se connecter sur un noeud du cluster puis:
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- charger l'environnement snakemake:
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module load snakemake/snakemake-8.4.6
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module load nodes/mafft-7.475
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- executer le programme, se placer dans ce dossier et:
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snakemake --cores 1
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| exercise0_improved_after_1B/samples.yaml | ||
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samples: ["P01325", "P01308"]
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Also available in: Unified diff
add exercise 0 improved after applying what was learnt in exercise 1B