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Nextflow pipeline to compute average metrics from reads that overlap a given set of positions

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bametrics-nf

Nextflow pipeline to compute average metrics from reads that overlap a given set of positions

Dependencies

  1. Install nextflow.

    curl -fsSL get.nextflow.io | bash

    And move it to a location in your $PATH (/usr/local/bin for example here):

    sudo mv nextflow /usr/local/bin

Input files and options

Command line example:

nextflow run bametrics.nf --bam_folder BAM/ --input_positions positions_by_sample.txt --output_file bametrics_output.txt

Options:

Parameter Default value Description
required
bam_folder - Folder containing BAM for each sample you want metrics on position
input_positions - File containing position-sample, in line-form "chr pos sample"
optional
nb_chunks 1 Value defining the number of parallelized processed chunks
output_file bametrics_output.txt File name of the output
out_folder . Output directory
metrics "AS" List of bam metrics, comma delimited

Pipeline execution DAG

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Nextflow pipeline to compute average metrics from reads that overlap a given set of positions

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