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main.nf
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main.nf
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include { FASTQC } from './modules/fastqc.nf'
include { MULTIQC } from './modules/multiqc.nf'
log.info """\
BASIC FASTQ FILE QC - N F P I P E L I N E
============================================
input_reads_path : ${params.input_dir}
output_dir : ${params.output_dir}
"""
.stripIndent()
workflow {
reads_ch = Channel.fromFilePairs("$params.input_dir/*{1,2}.fastq.gz").dump(tag:'Input Reads')
fastqc_ch = FASTQC(reads_ch)
MULTIQC(fastqc_ch)
}
workflow.onComplete {
println ( workflow.success ? """
Pipeline execution summary
---------------------------
Completed at: ${workflow.complete}
Duration : ${workflow.duration}
Success : ${workflow.success}
workDir : ${workflow.workDir}
exit status : ${workflow.exitStatus}
""" : """
Failed: ${workflow.errorReport}
exit status : ${workflow.exitStatus}
"""
)
}