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Fix itsx log file
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mdehollander committed Oct 1, 2018
1 parent 443148d commit c064598
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2 changes: 1 addition & 1 deletion Snakefile
Original file line number Diff line number Diff line change
Expand Up @@ -310,7 +310,7 @@ if config['its'] == True:
conda: "envs/itsx.yaml"
# TODO: Filter on specific list of organisms?
# Only ITS2 region?
shell: "ITSx --cpu {threads} --preserve TRUE -i {input.fasta} -o {params.basename} > {params.dir}/{log}"
shell: "ITSx --cpu {threads} --preserve TRUE -i {input.fasta} -o {params.basename} 2> {log}"

# Combine per sample files to a single project file
rule mergefiles:
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