117 lines
2.7 KiB
Plaintext
117 lines
2.7 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.
|
|
|
|
import groovy.json.JsonBuilder
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { fastq_ingress } from './lib/fastqingress'
|
|
|
|
|
|
process summariseReads {
|
|
// concatenate fastq and fastq.gz in a dir
|
|
|
|
label "pysam"
|
|
cpus 1
|
|
input:
|
|
tuple path(directory), val(sample_name)
|
|
output:
|
|
path "${sample_name}.stats"
|
|
shell:
|
|
"""
|
|
fastcat -s ${sample_name} -r ${sample_name}.stats -x ${directory} > /dev/null
|
|
"""
|
|
}
|
|
|
|
|
|
process getVersions {
|
|
label "pysam"
|
|
cpus 1
|
|
output:
|
|
path "versions.txt"
|
|
script:
|
|
"""
|
|
python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
|
|
fastcat --version | sed 's/^/fastcat,/' >> versions.txt
|
|
"""
|
|
}
|
|
|
|
process getParams {
|
|
label "pysam"
|
|
cpus 1
|
|
output:
|
|
path "params.json"
|
|
script:
|
|
def paramsJSON = new JsonBuilder(params).toPrettyString()
|
|
"""
|
|
# Output nextflow params object to JSON
|
|
echo '$paramsJSON' > params.json
|
|
"""
|
|
}
|
|
|
|
process makeReport {
|
|
label "pysam"
|
|
input:
|
|
path "seqs.txt"
|
|
path "versions/*"
|
|
path "params.json"
|
|
output:
|
|
path "wf-template-*.html"
|
|
script:
|
|
// report naming
|
|
report_name = "wf-template-" + params.report_name + '.html'
|
|
"""
|
|
report.py $report_name --versions versions seqs.txt --params params.json
|
|
"""
|
|
}
|
|
|
|
|
|
// See https://github.com/nextflow-io/nextflow/issues/1636
|
|
// This is the only way to publish files from a workflow whilst
|
|
// decoupling the publish from the process steps.
|
|
process output {
|
|
// publish inputs to output directory
|
|
label "pysam"
|
|
publishDir "${params.out_dir}", mode: 'copy', pattern: "*"
|
|
input:
|
|
path fname
|
|
output:
|
|
path fname
|
|
"""
|
|
echo "Writing output files"
|
|
"""
|
|
}
|
|
|
|
|
|
// workflow module
|
|
workflow pipeline {
|
|
take:
|
|
reads
|
|
main:
|
|
summary = summariseReads(reads)
|
|
software_versions = getVersions()
|
|
workflow_params = getParams()
|
|
report = makeReport(summary, software_versions.collect(), workflow_params)
|
|
emit:
|
|
summary.concat(report)
|
|
}
|
|
|
|
// entrypoint workflow
|
|
WorkflowMain.initialise(workflow, params, log)
|
|
workflow {
|
|
|
|
samples = fastq_ingress(
|
|
params.fastq, params.out_dir, params.samples, params.sanitize_fastq)
|
|
|
|
results = pipeline(samples)
|
|
output(results)
|
|
}
|