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check for newlines when concat fastas #53

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Feb 28, 2022
Merged

check for newlines when concat fastas #53

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3 changes: 2 additions & 1 deletion modules/get_host.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -56,11 +56,12 @@ process check_own {
"""
# -L for following a symbolic link
if ! ( file -L $fasta | grep -q 'gzip compressed' ); then
sed -i -e '\$a\\' ${fasta}
bgzip -@ ${task.cpus} < ${fasta} > ${fasta}.gz
# now $fasta'.gz'
else
mv ${fasta} ${fasta}.tmp
zcat ${fasta}.tmp | bgzip -@ ${task.cpus} -c > ${fasta}.gz
zcat ${fasta}.tmp | sed -e '\$a\\' | bgzip -@ ${task.cpus} -c > ${fasta}.gz
fi
"""
}
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