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Use gunzip (gzip) over zcat for MacOS compatibility #4

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Use gunzip (gzip) over zcat for MacOS compatibility #4

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2 changes: 1 addition & 1 deletion snakefile.smk
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Expand Up @@ -236,7 +236,7 @@ rule get_contig_names:
benchmark: config.get("benchmark", "benchmark/") + "{key}_" + rulename
log: config.get("log", f"{str(OUTDIR)}/log/") + "{key}_" + rulename
shell:
"zcat {input} | grep '>' | sed 's/>//' > {output} 2> {log} "
"gunzip -dc {input} | grep '>' | sed 's/>//' > {output} 2> {log} "

# Run strobealign to get the abundances
rulename = "Strobealign_bam_default"
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