Unverified Commit ff65f167 authored by Jihed Chouaref's avatar Jihed Chouaref Committed by GitHub
Browse files

Update pre_processing.smk

corrected error in the alignment paired end
parent 52ffe199
...@@ -71,8 +71,8 @@ rule align: ...@@ -71,8 +71,8 @@ rule align:
shell("bowtie2 --very-sensitive --threads {threads} -x {params.index} \ shell("bowtie2 --very-sensitive --threads {threads} -x {params.index} \
-U {input.forward_read} | samtools view -Sb - > {output.bams} 2>{log}") -U {input.forward_read} | samtools view -Sb - > {output.bams} 2>{log}")
else: else:
shell("bowtie2 --very-sentitive --threads {threads} -x {params.index} \ shell("bowtie2 --very-sensitive --threads {threads} -x {params.index} \
-1 {input.forward_read} -2 {input.reverse_read} samtools view -Sb - > {output.bams} 2>{log}") -1 {input.forward_read} -2 {input.reverse_read} | samtools view -Sb - > {output.bams} 2>{log}")
rule sort: rule sort:
......
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