110 lines
2.5 KiB
Plaintext
110 lines
2.5 KiB
Plaintext
#!/usr/bin/env nextflow
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// Developer notes
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//
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// This template workflow provides a basic structure to copy in order
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// to create a new workflow. Current recommended pratices are:
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// i) create a simple command-line interface.
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// ii) include an abstract workflow scope named "pipeline" to be used
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// in a module fashion.
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// iii) a second concreate, but anonymous, workflow scope to be used
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// as an entry point when using this workflow in isolation.
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nextflow.enable.dsl = 2
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include { fastq_ingress } from './lib/fastqingress'
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def helpMessage(){
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log.info """
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Workflow template'
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Usage:
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nextflow run epi2melabs/wf-template [options]
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Script Options:
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--fastq DIR Path to FASTQ directory (required)
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--samples FILE CSV file with columns named `barcode` and `sample_name`
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(or simply a sample name for non-multiplexed data).
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--out_dir DIR Path for output (default: $params.out_dir)
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"""
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}
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process summariseReads {
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// concatenate fastq and fastq.gz in a dir
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label "pysam"
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cpus 1
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input:
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tuple path(directory), val(sample_name)
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output:
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path "${sample_name}.stats"
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shell:
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"""
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fastcat -s ${sample_name} -r ${sample_name}.stats -x ${directory} > /dev/null
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"""
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}
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process makeReport {
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label "pysam"
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input:
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path "seqs.txt"
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output:
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path "wf-template-report.html"
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"""
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report.py wf-template-report.html seqs.txt
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"""
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}
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// See https://github.com/nextflow-io/nextflow/issues/1636
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// This is the only way to publish files from a workflow whilst
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// decoupling the publish from the process steps.
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process output {
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// publish inputs to output directory
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label "pysam"
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publishDir "${params.out_dir}", mode: 'copy', pattern: "*"
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input:
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path fname
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output:
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path fname
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"""
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echo "Writing output files"
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"""
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}
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// workflow module
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workflow pipeline {
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take:
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reads
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main:
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summary = summariseReads(reads)
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report = makeReport(summary)
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emit:
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summary.concat(report)
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}
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// entrypoint workflow
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workflow {
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if (params.help) {
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helpMessage()
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exit 1
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}
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if (!params.fastq) {
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helpMessage()
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println("")
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println("`--fastq` is required")
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exit 1
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}
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samples = fastq_ingress(
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params.fastq, params.out_dir, params.samples, params.sanitize_fastq)
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results = pipeline(samples)
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output(results)
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}
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