Verified Commit 8aee48b9 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

mv test.sh file from docker_modules to nf_modules

parent d254a0d5
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$fasta_from_bed {
container = "bedtools:2.25.0"
}
}
}
sge {
process{
$fasta_from_bed {
beforeScript = "module purge; module load BEDtools/2.25.0"
}
}
}
}
/*
* bedtools :
* Imputs : fastq files
* Output : fastq files
*/
/* fasta extraction */
params.fastq = "$baseDir/data/fasta/*.fasta"
params.bed = "$baseDir/data/annot/*.bed"
log.info "fasta file : ${params.fasta}"
log.info "bed file : ${params.bed}"
Channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
.set { fasta_files }
Channel
.fromPath( params.bed )
.ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
.set { bed_files }
process fasta_from_bed {
tag "$pair_id"
cpus 4
publishDir "results/fasta/", mode: 'copy'
input:
file fasta from fasta_files
file bed from bed_files
output:
file "*_extracted.fasta" into fasta_files_extracted
script:
"""
bedtools getfasta -name \
-fi ${fasta} -bed ${bed} -fo ${fasta.baseName}_extracted.fasta
"""
}
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