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illumina.config
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illumina.config
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// Illumina Parameters
params {
// Illumina fastq reads directory, can be singular or paired
directory = false
// Human bwa-mem indexs folder (so that they don't have to be made)
human_bwa_index = false
// Minimum mapping quality of the reads to keep
keep_min_map_quality = 60
// Minimum mapping quality of the reads to remove
remove_min_map_quality = 0
// Minimum fastq read length (unused currently)
min_length = 50
// Maximum fastq read length (unused currently)
max_length = 300
// Single-end reads as input
single_end = false
// illumina fastq search path
illuminaSuffixes = ['*_R{1,2}_001', '*_R{1,2}', '*_{1,2}', '*pair{1,2}' ]
fastqpaths = makeFastqPaths( params.illuminaSuffixes )
}
def makeFastqPaths ( illuminaSuffixes ) {
def fastq_searchpath = []
for (suffix in illuminaSuffixes){
fastq_searchpath.add(params.directory.toString() + '/**' + suffix.toString() + '.fastq')
}
return fastq_searchpath
}