jpayne@68: BBTools Config File Readme
jpayne@68: Written by Brian Bushnell
jpayne@68: Last updated May 12, 2015
jpayne@68: 
jpayne@68: A config file is a text file with a set of parameters that will be added to the command line.
jpayne@68: The format is one parameter per line, with the # symbol indicating comments.
jpayne@68: To use a config file, use the config=file flag.  For example, take BBDuk:
jpayne@68: 
jpayne@68: bbduk.sh in=reads.fq out=trimmed.fq ref=ref.fa k=23 mink=11 hdist=1 tbo tpe
jpayne@68: 
jpayne@68: That is equivalent to:
jpayne@68: 
jpayne@68: bbduk.sh in=reads.fq out=trimmed.fq ref=ref.fa config=trimadapters.txt
jpayne@68: ...if trimadapters.txt contained these lines:
jpayne@68: k=23
jpayne@68: mink=11
jpayne@68: hdist=1
jpayne@68: tbo
jpayne@68: tpe
jpayne@68: 
jpayne@68: 
jpayne@68: Any parameter placed AFTER the config file will override the same parameter if it is in the config file.  
jpayne@68: For example, in this case k=20 will be used:
jpayne@68: bbduk.sh in=reads.fq out=trimmed.fq ref=ref.fa config=trimadapters.txt k=20
jpayne@68: 
jpayne@68: But in this case, k=23 will be used, from the config file:
jpayne@68: bbduk.sh in=reads.fq out=trimmed.fq ref=ref.fa k=20 config=trimadapters.txt
jpayne@68: 
jpayne@68: What are config files for?  Well, mainly, to overcome difficulties like whitespace in file paths, or command lines that are too long.
jpayne@68: There are some example config files in bbmap/config/.  They are not used unless you specifically tell a program to use them.