109 lines
2.2 KiB
Plaintext
109 lines
2.2 KiB
Plaintext
#!/usr/bin/env nextflow
|
|
|
|
// Developer notes
|
|
//
|
|
// This template workflow provides a basic structure to copy in order
|
|
// to create a new workflow. Current recommended pratices are:
|
|
// i) create a simple command-line interface.
|
|
// ii) include an abstract workflow scope named "pipeline" to be used
|
|
// in a module fashion.
|
|
// iii) a second concreate, but anonymous, workflow scope to be used
|
|
// as an entry point when using this workflow in isolation.
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
|
|
def helpMessage(){
|
|
log.info """
|
|
Workflow template'
|
|
|
|
Usage:
|
|
nextflow run epi2melabs/wf-template [options]
|
|
|
|
Script Options:
|
|
--fastq DIR Path to directory containing FASTQ files (required)
|
|
--out_dir DIR Path for output (default: $params.out_dir)
|
|
"""
|
|
}
|
|
|
|
|
|
process readSeqs {
|
|
// Just write a file with sequence lengths
|
|
label "pysam"
|
|
input:
|
|
file reads
|
|
output:
|
|
file "seqs.txt"
|
|
|
|
"""
|
|
read_lengths.py $reads seqs.txt
|
|
"""
|
|
}
|
|
|
|
|
|
process makeReport {
|
|
label "pysam"
|
|
input:
|
|
file "seqs.txt"
|
|
output:
|
|
file "report.html"
|
|
"""
|
|
report.py report.html seqs.txt
|
|
"""
|
|
}
|
|
|
|
|
|
// See https://github.com/nextflow-io/nextflow/issues/1636
|
|
// This is the only way to publish files from a workflow whilst
|
|
// decoupling the publish from the process steps.
|
|
process output {
|
|
// publish inputs to output directory
|
|
|
|
publishDir "${params.out_dir}", mode: 'copy', pattern: "*"
|
|
input:
|
|
file fname
|
|
output:
|
|
file fname
|
|
"""
|
|
echo "Writing output files"
|
|
"""
|
|
}
|
|
|
|
|
|
// workflow module
|
|
workflow pipeline {
|
|
take:
|
|
reads
|
|
main:
|
|
summary = readSeqs(reads)
|
|
report = makeReport(summary)
|
|
emit:
|
|
summary.concat(report)
|
|
}
|
|
|
|
// entrypoint workflow
|
|
workflow {
|
|
|
|
if (params.help) {
|
|
helpMessage()
|
|
exit 1
|
|
}
|
|
|
|
if (!params.fastq) {
|
|
helpMessage()
|
|
println("")
|
|
println("`--fastq` is required")
|
|
exit 1
|
|
}
|
|
|
|
|
|
reads = file("$params.fastq/*.fastq*", type: 'file', maxdepth: 1)
|
|
if (reads) {
|
|
reads = Channel.fromPath(params.fastq, type: 'dir', maxDepth: 1)
|
|
results = pipeline(reads)
|
|
output(results)
|
|
} else {
|
|
println("No .fastq(.gz) files found under `${params.fastq}`.")
|
|
}
|
|
}
|