A set of nice utility methods for use with Nextflow pipelines
This plugin is currently under construction. Please see the details in NOTES.md
for development and usage. And check out examples/test.nf
to see how the plugin is used in a Nextflow pipeline.
An example workflow is included so you can see how the plugin can be used.
Run the basic workflow with
nextflow run examples/test.nf
You will get the following files
output/software_versions_mqc.yaml
: a software versions table for use with MultiQCoutput/workflow_summary_mqc.yaml
: a workflow summary table for use with MultiQC
If you have Docker running you can run the full example
nextflow run examples/test.nf -profile multiqc
This will also give you the following file
output/multiqc_report.html
: a MultiQC report that utilizes the created tables
Some examples of the output are included in the repo here at examples/example_output
.
To use it with your own pipeline, currently you will need to make sure to include it in your nextflow.config
;
plugins {
id 'nf-niceutils'
}
and run it like this
NXF_PLUGINS_TEST_REPOSITORY=https://github.com/raw/stevekm/nextflow-plugins-registry/main/plugins.json nextflow run main.nf
Some time soon hopefully I can get it pushed into the official Nextflow registry :)
(these are subject to change)
The following methods are the most useful ones offered by the plugin;
createProcessVersionFromYAMLstrList
: creates a MultiQC Software Versions Table YAML with embedded HTML tableworkflowSummaryTableStr
: creates a workflow summary table YAML for use with MultiQC
You can see examples of how to use each function inside the examples/test.nf
script.
// create a MultiQC Software Versions Table YAML + HTML
// versions_ch contains versions.yml files output by Nextflow processes
mqc_versions_ch = versions_ch.map{ it.text }
.collect()
.map{ versions ->
def processList = createProcessVersionFromYAMLstrList(versions)
makeVersionsYAML(
processList,
workflow.manifest.name,
workflow.manifest.homePage,
workflow.manifest.version,
workflow.nextflow.version.toString()
)
}.collectFile(storeDir: "${params.outdir}", name: "software_versions_mqc.yaml")
// create a workflow summary table
workflow_summary_ch = Channel.from(
workflowSummaryTableStr(
params,
workflow.properties,
workflow.manifest.properties,
['foo_key'] // some 'bad params' to exclude from the output
)
).collectFile(storeDir: "${params.outdir}", name: "workflow_summary_mqc.yaml")