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author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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jpayne@68 1 BBTools Config File Readme
jpayne@68 2 Written by Brian Bushnell
jpayne@68 3 Last updated May 12, 2015
jpayne@68 4
jpayne@68 5 A config file is a text file with a set of parameters that will be added to the command line.
jpayne@68 6 The format is one parameter per line, with the # symbol indicating comments.
jpayne@68 7 To use a config file, use the config=file flag. For example, take BBDuk:
jpayne@68 8
jpayne@68 9 bbduk.sh in=reads.fq out=trimmed.fq ref=ref.fa k=23 mink=11 hdist=1 tbo tpe
jpayne@68 10
jpayne@68 11 That is equivalent to:
jpayne@68 12
jpayne@68 13 bbduk.sh in=reads.fq out=trimmed.fq ref=ref.fa config=trimadapters.txt
jpayne@68 14 ...if trimadapters.txt contained these lines:
jpayne@68 15 k=23
jpayne@68 16 mink=11
jpayne@68 17 hdist=1
jpayne@68 18 tbo
jpayne@68 19 tpe
jpayne@68 20
jpayne@68 21
jpayne@68 22 Any parameter placed AFTER the config file will override the same parameter if it is in the config file.
jpayne@68 23 For example, in this case k=20 will be used:
jpayne@68 24 bbduk.sh in=reads.fq out=trimmed.fq ref=ref.fa config=trimadapters.txt k=20
jpayne@68 25
jpayne@68 26 But in this case, k=23 will be used, from the config file:
jpayne@68 27 bbduk.sh in=reads.fq out=trimmed.fq ref=ref.fa k=20 config=trimadapters.txt
jpayne@68 28
jpayne@68 29 What are config files for? Well, mainly, to overcome difficulties like whitespace in file paths, or command lines that are too long.
jpayne@68 30 There are some example config files in bbmap/config/. They are not used unless you specifically tell a program to use them.