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agillenCopilot
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Update rules/cutadapt_star.snake
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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rules/cutadapt_star.snake

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@@ -129,7 +129,7 @@ rule cutadapt_paired:
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echo "removing internal seq..."
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cutadapt --discard-untrimmed --info-file {params.info} -o /dev/null -p {params.temp2} -g {params.bc_cut} =(cat {input}) =(cat $(echo {input} | sed 's/_R1/_R2/g'))
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echo "stitching R1 FASTQ back together..."
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if [ -z {params.bc_length1} ];
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if [ -z "{params.bc_length1}" ];
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then
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python3 inst/scripts/cut_paste_fastq.py -i {params.info} -o {params.temp}
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else

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