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View Code? Open in Web Editor NEWA snakemake workflow for downstream processing of WGS
A snakemake workflow for downstream processing of WGS
Testing issue and what the hell is this about.... :(
You have helper scripts in /data/sacgf/microbio/lleong/commands/
These should be in the github repo?
You may want to use the more portable seqtk seq -L 1000 in.fna > out.fna
for this.
rule remove_small:
input:
"{sample}/shovill"
output:
"filtered_contigs/{sample}.fna"
shell:
"perl /data/sacgf/microbio/lleong/commands/removesmalls.pl 1000 {input}/contigs.fa > {output}"
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