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modules/01_prepare_bam.nf

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@@ -5,6 +5,7 @@ params.index_memory = "8g"
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params.platform = "ILLUMINA"
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params.output = 'output'
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/*
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This step sets MAPQ to 0 for all unmapped reads + avoids soft clipping beyond the end of the reference genome
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This step reorders chromosomes in the BAM file according to the provided reference (this step is required for GATK)

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