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Commit f31a8f3e authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
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fix typo error in paired end mode

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......@@ -70,10 +70,10 @@ rule sortmerna:
if [[ ${{#infiles[@]}} -eq 2 ]];
then
sortmerna --ref ${{fasta}} --idx-dir ${{idxdir}} --workdir {params.tmpdir}/{wildcards.SAMPLE} -threads {threads} --reads ${{infiles[0]}} --reads ${{infiles[1]}} --aligned out_paired_ribo --fastx --out2 --paired_out --other out_paired -v > {log.out} 2> {log.err}
mv out_paired_fwd.fq${{ext}} {{outnorRNA[0]}}
mv out_paired_rev.fq${{ext}} {{outnorRNA[1]}}
mv out_paired_ribo_fwd.fq${{ext}} {{outrRNA[0]}}
mv out_paired_ribo_rev.fq${{ext}} {{outrRNA[1]}}
mv out_paired_fwd.fq${{ext}} ${{outnorRNA[0]}}
mv out_paired_rev.fq${{ext}} ${{outnorRNA[1]}}
mv out_paired_ribo_fwd.fq${{ext}} ${{outrRNA[0]}}
mv out_paired_ribo_rev.fq${{ext}} ${{outrRNA[1]}}
#mv output.rRNA.log {log.out}
else
......
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