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Revision 66c1b9ca

Added by Chloé QUIGNOT over 1 year ago

add exercise 0 improved after applying what was learnt in exercise 1A

View differences:

exercise0_improved_after_1A/Snakefile
samples=["P01325", "P01308"]
# Update 1: we created a target rule containing the final
# output and intermediate outputs of our pipeline
# Update 2: we used the expand function to generalise our target
# rule, reading from a Python list of UniProt ids
rule targets:
input:
expand("fasta/{sample}.fasta", sample=samples),
"fusionFasta/allSequences.fasta",
"mafft/mafft_res.fasta",
# Update 3: we generalised the loadData rule using a wildcard
# called "sample" and we access it within the shell
# directive using the wildcards variable
# i.e. {wildcards.sample}
rule loadData:
output:
"fasta/{sample}.fasta",
shell:
"""
wget --directory-prefix $(dirname {output}) \
https://www.uniprot.org/uniprot/{wildcards.sample}.fasta
"""
# Update 4: we generalised the fusionFasta rule using the
# the expand function, similar to the target rule
rule fusionFasta:
input:
expand("fasta/{sample}.fasta", sample=samples),
output:
"fusionFasta/allSequences.fasta",
shell:
"""
cat {input} > {output}
"""
# Update 5: the mafft rule will be executed even if it's at
# the end of the code, because the target rule
# specifies the final outputs that we expect
rule mafft:
input:
"fusionFasta/allSequences.fasta",
output:
"mafft/mafft_res.fasta",
shell:
"""
mafft {input} > {output}
"""
exercise0_improved_after_1A/readme_runSnake.txt
Pour faire fonctionner le pipeline il faut se connecter sur un noeud du cluster puis:
- charger l'environnement snakemake:
module load snakemake/snakemake-8.4.6
module load nodes/mafft-7.475
- executer le programme, se placer dans ce dossier et:
snakemake --cores 1

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