wildcards problem - Githubissues

thkuo / seq2geno

Computational pipeline for genomic features of bacterial population

GNU General Public License v3.0

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wildcards problem #19

Open thkuo opened 6 years ago

thkuo commented 6 years ago

In a rule, all the output files should use the same wildcards to avoid incorrect writing.

How to start correcting?
How to fit the current scripts to this requirement while ensuring the correct dependencies?
How to avoid wildcard multi-match problem? (ie. "{sample}.tmp.fa" may be incorrectly matched by "{sample}.fa") -> Try single and simple extensions at every level (folder)

thkuo commented 6 years ago

check #6

thkuo commented 6 years ago

check #7

thkuo commented 6 years ago

check #1

thkuo commented 6 years ago

Possible solution for now: the file names should include no wildcards, but the path (eg. folder) can be. For example,

rule process_vcf:
    ...
    output:
        vcf_gz={TMP_D}/{strain}/{mapper}/vcf.gz

is better (so far) than

rule process_vcf:
    ...
    output:
        vcf_gz={TMP_D}/{strain}/{mapper}.vcf.gz

Use the DAG plot to check where in the dependent .smk files should also be updated First test in the commit da5e455239592de08e75b8d433598f8553527b75