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Phil Ewels 2020-07-11 13:27:56 +02:00 committed by GitHub
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tools/bowtie2/main.nf
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@ -45,10 +45,7 @@ process BOWTIE2 {
index = params.genome["bowtie2"] index = params.genome["bowtie2"]
bowtie2_name = name + "_" + params.genome["name"] bowtie2_name = name + "_" + params.genome["name"]
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")
""" """
module load bowtie2
module load samtools
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 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
""" """