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@ -45,10 +45,7 @@ process BOWTIE2 {
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index = params.genome["bowtie2"]
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bowtie2_name = name + "_" + params.genome["name"]
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println ("bowtie2 -x ${index} -p ${cores} ${bowtie2_options} ${readString} 2>${bowtie2_name}_bowtie2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${bowtie2_name}_bowtie2.bam")
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"""
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module load bowtie2
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module load samtools
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bowtie2 -x ${index} -p ${cores} ${bowtie2_options} ${readString} 2>${bowtie2_name}_bowtie2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${bowtie2_name}_bowtie2.bam
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"""
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