Added custom version dump module that has better version output (be1f559c) · Commits · Chaos / Cutandrun

assets/multiqc_config.yaml

+6 −0

Original line number	Diff line number	Diff line
		@@ -46,6 +46,12 @@ module_order:
		- picard
		- custom_content

		custom_content:
		order:
		- fragment_lengths
		- software_versions
		- software_versions_unique

		# Don't show % Dups in the General Stats table (we have this from Picard)
		table_columns_visible:
		FastQC:

modules.json

+0 −3

Original line number	Diff line number	Diff line
		@@ -27,9 +27,6 @@
		"cat/fastq": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"custom/dumpsoftwareversions": {
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"deeptools/computematrix": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},

modules/nf-core/modules/custom/dumpsoftwareversions/functions.nf→modules/local/modules/custom/dumpsoftwareversions/functions.nf

+0 −0

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modules/nf-core/modules/custom/dumpsoftwareversions/main.nf→modules/local/modules/custom/dumpsoftwareversions/main.nf

+66 −5

Original line number	Diff line number	Diff line
		@@ -24,7 +24,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
		output:
		path "software_versions.yml" , emit: yml
		path "software_versions_mqc.yml" , emit: mqc_yml
		path "versions.yml" , emit: versions
		path "software_versions_unique_mqc.yml", emit: mqc_unique_yml
		path "local_versions.yml" , emit: versions

		script:
		"""
		@@ -72,6 +73,53 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
		html.append("</table>")
		return "\\n".join(html)

		def _make_versions_unique_html(versions):
		unique_versions = []

		for process, tmp_versions in sorted(versions.items()):
		for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
		tool_version = tool + "=" + version
		if tool_version not in unique_versions:
		unique_versions.append(tool_version)

		unique_versions.sort()

		html = [
		dedent(
		'''\\
		<style>
		#nf-core-versions-unique tbody:nth-child(even) {
		background-color: #f2f2f2;
		}
		</style>
		<table class="table" style="width:100%" id="nf-core-versions-unique">
		<thead>
		<tr>
		<th> Software </th>
		<th> Version </th>
		</tr>
		</thead>
		'''
		)
		]

		for tool_version in unique_versions:
		tool_version_split = tool_version.split('=')
		html.append("<tbody>")
		html.append(
		dedent(
		f'''\\
		<tr>
		<td><samp>{tool_version_split[0]}</samp></td>
		<td><samp>{tool_version_split[1]}</samp></td>
		</tr>
		'''
		)
		)
		html.append("</tbody>")
		html.append("</table>")
		return "\\n".join(html)

		module_versions = {}
		module_versions["${getProcessName(task.process)}"] = {
		'python': platform.python_version(),
		@@ -88,19 +136,32 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {

		versions_mqc = {
		'id': 'software_versions',
		'section_name': '${workflow.manifest.name} Software Versions',
		'section_name': '${workflow.manifest.name} Software Versions by Process',
		'section_href': 'https://github.com/${workflow.manifest.name}',
		'plot_type': 'html',
		'description': 'are collected at run time from the software output.',
		'data': _make_versions_html(workflow_versions)
		}

		versions_mqc_unique = {
		'id': 'software_versions_unique',
		'section_name': '${workflow.manifest.name} Software Versions',
		'section_href': 'https://github.com/${workflow.manifest.name}',
		'plot_type': 'html',
		'description': 'are collected at run time from the software output.',
		'data': _make_versions_unique_html(workflow_versions)
		}

		with open("software_versions.yml", 'w') as f:
		yaml.dump(workflow_versions, f, default_flow_style=False)

		with open("software_versions_mqc.yml", 'w') as f:
		yaml.dump(versions_mqc, f, default_flow_style=False)

		with open('versions.yml', 'w') as f:
		with open("software_versions_unique_mqc.yml", 'w') as f:
		yaml.dump(versions_mqc_unique, f, default_flow_style=False)

		with open('local_versions.yml', 'w') as f:
		yaml.dump(module_versions, f, default_flow_style=False)
		"""
		}

modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml→modules/local/modules/custom/dumpsoftwareversions/meta.yml

+0 −0

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