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elabaron authored
Changes to be committed: new file: src/10_ribowave.nf modified: src/docker_modules/FastQC/0.11.5/Dockerfile : Add perl instalation new file: src/nf_modules/FastQC/fastqc.config new file: src/nf_modules/FastQC/fastqc.nf renamed: src/nf_modules/Ribowave/10_ribowave.nf -> src/nf_modules/Ribowave/pipeline_PSMN.nf new file: src/nf_modules/Ribowave/pipeline_docker.nf modified: src/nf_modules/Ribowave/test/P-site.nf new file: src/ribowave.config
fastqc.nf 585 B
/*
* fastqc :
* Imputs : fastq files
* Output : pdf files
*/
/* fastQC */
params.fastq = ""
log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process fastqc {
tag "$fastq.baseName"
publishDir "results/fasqc/${fastq.baseName}/", mode: 'copy'
input:
file fastq from fastq_files
output:
file "*" into fastqc_repport
script:
"""
fastqc -o ./ --noextract -f fastq ${fastq}
"""
}