Revision 66c1b9ca
Added by Chloé QUIGNOT 7 months ago
| exercise0_improved_after_1A/Snakefile | ||
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samples=["P01325", "P01308"]
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# Update 1: we created a target rule containing the final
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# output and intermediate outputs of our pipeline
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# Update 2: we used the expand function to generalise our target
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# rule, reading from a Python list of UniProt ids
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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 3: we generalised the loadData rule using a wildcard
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# called "sample" and we access it within the shell
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# directive using the wildcards variable
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# i.e. {wildcards.sample}
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rule loadData:
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output:
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"fasta/{sample}.fasta",
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shell:
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"""
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wget --directory-prefix $(dirname {output}) \
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https://www.uniprot.org/uniprot/{wildcards.sample}.fasta
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"""
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# Update 4: we generalised the fusionFasta rule using the
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# the expand function, similar to the target rule
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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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shell:
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"""
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cat {input} > {output}
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"""
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# Update 5: the mafft rule will be executed even if it's at
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# the end of the code, because the target rule
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# specifies the final outputs that we expect
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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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shell:
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"""
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mafft {input} > {output}
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"""
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| exercise0_improved_after_1A/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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Also available in: Unified diff
add exercise 0 improved after applying what was learnt in exercise 1A