Migrate template to nf-core-utils plugin #3790
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -20,23 +20,7 @@ | |
| } | ||
| }, | ||
| "subworkflows": { | ||
| "nf-core": {} | ||
| } | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -8,18 +8,24 @@ | |
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| */ | ||
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| {% if nf_schema %}include { paramsSummaryLog } from 'plugin/nf-schema' | ||
| include { validateParameters } from 'plugin/nf-schema' | ||
| include { paramsSummaryMap } from 'plugin/nf-schema' | ||
| include { samplesheetToList } from 'plugin/nf-schema'{% endif %} | ||
| {%- if email %} | ||
| include { completionEmail } from 'plugin/nf-core-utils' | ||
| {%- endif %} | ||
| include { completionSummary } from 'plugin/nf-core-utils' | ||
| {%- if adaptivecard or slackreport %} | ||
| include { imNotification } from 'plugin/nf-core-utils' | ||
| {%- endif %} | ||
| include { checkConfigProvided } from 'plugin/nf-core-utils' | ||
| include { checkProfileProvided } from 'plugin/nf-core-utils' | ||
| include { getWorkflowVersion } from 'plugin/nf-core-utils' | ||
| include { dumpParametersToJSON } from 'plugin/nf-core-utils' | ||
| include { checkCondaChannels } from 'plugin/nf-core-utils' | ||
| include { processVersionsFromFile } from 'plugin/nf-core-utils' | ||
| include { workflowVersionToChannel } from 'plugin/nf-core-utils' | ||
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| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
|
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@@ -44,31 +50,36 @@ workflow PIPELINE_INITIALISATION { | |
| // | ||
| // Print version and exit if required and dump pipeline parameters to JSON file | ||
| // | ||
| if (version) { | ||
| log.info("${workflow.manifest.name} ${getWorkflowVersion(workflow.manifest.version, workflow.commitId)}") | ||
| System.exit(0) | ||
| } | ||
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| if (outdir) { | ||
| dumpParametersToJSON(outdir, params) | ||
| } | ||
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| if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { | ||
| checkCondaChannels() | ||
| } | ||
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| {%- if nf_schema %} | ||
|
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| // | ||
| // Validate parameters and generate parameter summary to stdout | ||
| // | ||
| log.info paramsSummaryLog(workflow) | ||
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| if (validate_params) { | ||
| validateParameters() | ||
| } | ||
| {%- endif %} | ||
|
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| // | ||
| // Check config provided to the pipeline | ||
| // | ||
| checkConfigProvided() | ||
| checkProfileProvided(nextflow_cli_args, monochrome_logs) | ||
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| {%- if igenomes %} | ||
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@@ -157,7 +168,7 @@ workflow PIPELINE_COMPLETION { | |
| plaintext_email, | ||
| outdir, | ||
| monochrome_logs, | ||
| {% if multiqc %}multiqc_reports.getVal(){% else %}[]{% endif %} | ||
| ) | ||
| } | ||
| {%- endif %} | ||
|
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@@ -182,6 +193,55 @@ workflow PIPELINE_COMPLETION { | |
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| */ | ||
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| // | ||
| // Get channel of software versions used in pipeline in YAML format | ||
| // | ||
| def softwareVersionsToYAML(ch_versions) { | ||
| return ch_versions.unique() | ||
| .map { version -> processVersionsFromFile([version.toString()]) } | ||
| .unique() | ||
| .mix(Channel.fromList(workflowVersionToChannel(workflow.session)).map { it -> | ||
| """ | ||
| Workflow: | ||
| ${it[1]}: ${it[2]} | ||
| """.stripIndent().trim() | ||
| }) | ||
| } | ||
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| // | ||
| // Get workflow summary for MultiQC | ||
| // | ||
| def paramsSummaryMultiqc(summary_params) { | ||
|
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There was a problem hiding this comment. wrap this whole function inside a |
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| def summary_section = '' | ||
| summary_params | ||
| .keySet() | ||
| .each { group -> | ||
| def group_params = summary_params.get(group) | ||
| // This gets the parameters of that particular group | ||
| if (group_params) { | ||
| summary_section += " <p style=\"font-size:110%\"><b>${group}</b></p>\n" | ||
| summary_section += " <dl class=\"dl-horizontal\">\n" | ||
| group_params | ||
| .keySet() | ||
| .sort() | ||
| .each { param -> | ||
| summary_section += " <dt>${param}</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n" | ||
| } | ||
| summary_section += " </dl>\n" | ||
| } | ||
| } | ||
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| def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String | ||
| yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" | ||
| yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" | ||
| yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" | ||
| yaml_file_text += "plot_type: 'html'\n" | ||
| yaml_file_text += "data: |\n" | ||
| yaml_file_text += "${summary_section}" | ||
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| return yaml_file_text | ||
| } | ||
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| {%- if igenomes %} | ||
| // | ||
| // Check and validate pipeline parameters | ||
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needs a
{% if email %}wrapper