mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
58 lines
1.6 KiB
Text
58 lines
1.6 KiB
Text
nextflow.preview.dsl=2
|
|
params.genome = ''
|
|
|
|
process HISAT2 {
|
|
// depending on the genome used one might want/need to adjust the memory settings.
|
|
// For the E. coli test data this is probably not required
|
|
// label 'bigMem'
|
|
// label 'multiCore'
|
|
|
|
publishDir "$outdir/hisat2",
|
|
mode: "copy", overwrite: true
|
|
|
|
input:
|
|
tuple val(name), path(reads)
|
|
val outdir
|
|
val hisat2_args
|
|
val verbose
|
|
|
|
output:
|
|
path "*bam", emit: bam
|
|
path "*stats.txt", emit: stats
|
|
|
|
script:
|
|
|
|
if (verbose){
|
|
println ("[MODULE] HISAT2 ARGS: " + hisat2_args)
|
|
}
|
|
|
|
cores = 4
|
|
readString = ""
|
|
hisat_options = hisat2_args
|
|
|
|
// Options we add are
|
|
hisat_options = hisat_options + " --no-unal --no-softclip "
|
|
|
|
if (reads instanceof List) {
|
|
readString = "-1 "+reads[0]+" -2 "+reads[1]
|
|
hisat_options = hisat_options + " --no-mixed --no-discordant"
|
|
}
|
|
else {
|
|
readString = "-U "+reads
|
|
}
|
|
index = params.genome["hisat2"]
|
|
|
|
splices = ''
|
|
if (params.genome.containsKey("hisat2_splices")){
|
|
splices = " --known-splicesite-infile " + params.genome["hisat2_splices"]
|
|
}
|
|
else{
|
|
println ("No key 'hisat2_splices' was supplied. Skipping...")
|
|
}
|
|
hisat_name = name + "_" + params.genome["name"]
|
|
|
|
"""
|
|
hisat2 -p ${cores} ${hisat_options} -x ${index} ${splices} ${readString} 2>${hisat_name}_hisat2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${hisat_name}_hisat2.bam
|
|
"""
|
|
|
|
}
|