Commit 4974b176 authored by Celine Noirot's avatar Celine Noirot
Browse files

add soft version and summary in multiqc

parent 9dfddb08
......@@ -3,7 +3,9 @@ report_comment: >
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://forgemia.inra.fr/get-nextflow-ngl-bi/template-nf" target="_blank">documentation</a>.
report_section_order:
nf-core/template-software-versions:
software_versions:
order: -1000
summary:
order: -1001
export_plots: true
......@@ -5,13 +5,13 @@ import re
# TODO nf-core: Add additional regexes for new tools in process get_software_versions
regexes = {
'nf-core/template': ['v_pipeline.txt', r"(\S+)"],
'Pipeline': ['v_pipeline.txt', r"(\S+)"],
'Nextflow': ['v_nextflow.txt', r"(\S+)"],
'FastQC': ['v_fastqc.txt', r"FastQC v(\S+)"],
'MultiQC': ['v_multiqc.txt', r"multiqc, version (\S+)"],
}
results = OrderedDict()
results['nf-core/template'] = '<span style="color:#999999;\">N/A</span>'
results['Pipeline'] = '<span style="color:#999999;\">N/A</span>'
results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
results['FastQC'] = '<span style="color:#999999;\">N/A</span>'
results['MultiQC'] = '<span style="color:#999999;\">N/A</span>'
......@@ -35,8 +35,7 @@ for k in results:
# Dump to YAML
print ('''
id: 'software_versions'
section_name: 'nf-core/template Software Versions'
section_href: 'https://github.com/nf-core/template'
section_name: 'Software Versions'
plot_type: 'html'
description: 'are collected at run time from the software output.'
data: |
......
......@@ -228,6 +228,25 @@ process assembly {
"""
}
process workflow_summary {
output:
file 'workflow_summary_mqc.yaml' into ch_workflow_summary_yaml
exec:
def yaml_file = task.workDir.resolve('workflow_summary_mqc.yaml')
yaml_file.text = """
id: 'summary'
description: " - this information is collected when the pipeline is started."
section_name: 'Workflow Summary'
section_href: "${workflow.manifest.homePage}"
plot_type: 'html'
data: |
<dl class=\"dl-horizontal\">
${summary.collect { k,v -> " <dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }.join("\n")}
</dl>
""".stripIndent()
}
/*
* STEP - MultiQC
......@@ -243,8 +262,8 @@ process multiqc {
file (multiqc_config) from ch_multiqc_config
file ('fastqc/*') from ch_fastqc_results_for_multiqc.collect().ifEmpty([])
// TODO get-nf: Add in log files from your new processes for MultiQC to find!
//file ('softwareVersions/*') from softwareVersionsYamlCh.collect().ifEmpty([])
//file ('workflowSummary/*') from workflowSummaryYamlCh.collect()
file ('software_versions/*') from software_versions_yaml.collect()
file ('workflowSummary/*') from ch_workflow_summary_yaml.collect()
output:
file "*report.html" into ch_multiqc_report
......
......@@ -73,7 +73,7 @@ timeline {
trace {
enabled = true
file = "${params.tracedir}/execution_trace.txt"
fields = 'task_id,name,status,exit,realtime,%cpu,rss,script'
fields = 'task_id,name,status,exit,realtime,%cpu,rss'
}
report {
......
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