nf-core快速开发流程

安装

pip install nf-core

Creating a new pipeline

creating-a-new-pipeline

╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮
│ --name           -n  TEXT  The name of your new pipeline                                         │
│ --description    -d  TEXT  A short description of your pipeline                                  │
│ --author         -a  TEXT  Name of the main author(s)                                            │
│ --version            TEXT  The initial version number to use                                     │
│ --no-git                   Do not initialise pipeline as new git repository                      │
│ --force          -f        Overwrite output directory if it already exists                       │
│ --outdir         -o  TEXT  Output directory for new pipeline (default: pipeline name)            │
│ --template-yaml  -t  TEXT  Pass a YAML file to customize the template                            │
│ --plain                    Use the standard nf-core template                                     │
│ --help           -h        Show this message and exit.                                           │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯

nf-core create -n demo -d 'This is demo.' -a 'author' --plain

module

模块的本地仓库~/.config/nfcore/nf-core/modules

查看本地模块

nf-core modules --git-remote https://gitee.com/minebiome/modules.git list local

install module

nf-core modules  --git-remote https://gitee.com/minebiome/modules.git  install fastp

update module

nf-core modules  --git-remote https://gitee.com/minebiome/modules.git  update

remove module

nf-core modules --git-remote https://gitee.com/minebiome/modules.git   remove fastp

自定义函数

ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
	file(params.multiqc_methods_description, checkIfExists: true) : 
	file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)

methods_description    = WorkflowTest.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
 ch_methods_description = Channel.value(methods_description)

WorkflowTest.methodsDescriptionText

    public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) {
        // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
        def meta = [:]
        meta.workflow = run_workflow.toMap()
        meta["manifest_map"] = run_workflow.manifest.toMap()

        meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
        meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"

        def methods_text = mqc_methods_yaml.text

        def engine =  new SimpleTemplateEngine()
        def description_html = engine.createTemplate(methods_text).make(meta)

        return description_html
    }