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Bash best practices and style-guide

Just simple methods to keep the code clean.

Inspired by progrium/bashstyle and Kfir Lavi post.

Quick big rules

• All code goes in a function
• Always double quote variables

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#!/usr/bin/env Rscript
#PBS -V

# This script will call copy number variants using cn.mops
# usage: Rscript cn.mops.R --help

library(optparse)
 
option_list = list(
  make_option(c("-i", "--input_dir"), type="character", default=NULL, 

IdoBar

set -e, -u, -o, -x pipefail

The set lines

• These lines deliberately cause your script to fail. Wait, what? Believe me, this is a good thing.
• With these settings, certain common errors will cause the script to immediately fail, explicitly and loudly. Otherwise, you can get hidden bugs that are discovered only when they blow up in production.

• set -euxo pipefail is short for:

set -e
set -u

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#!/bin/bash

if [ $# -ne 1 ]; then
  echo "Usage: $0 <input_gtf_file>"
  exit 1
fi

input_gtf="$1"
output_prefix="output"
sorted_gtf="${output_prefix}.sorted.gtf"

IdoBar

#! /bin/bash

## See also https://github.com/nextflow-io/nextflow/discussions/4308

## cd to a parent directory for a Nextflow pipeline executation, i.e. contains .nextflow and work directories
WORKDIR=$1
## Find work directories essential to the last pipeline run, as absolute paths
nextflow log last > $WORKDIR/preserve_dirs.txt

## Find all work directories, as absolute paths

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#!/usr/bin/env bash

# usage function
function usage()
{
   cat << HEREDOC

   Usage: $progname [--threads NUM] [--con NUM] [--db STR] [--outdir STR] [--remove STR] [--verbose] [--list] [--extract] 

    optional arguments: