Skip to content

simplify TEMPLATE with nf-core-utils 0.4.0 #3870

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 2 commits into
base: dev
Choose a base branch
from
Open

simplify TEMPLATE with nf-core-utils 0.4.0 #3870

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
9391d7c
simplify TEMPLATE with nf-core-utils 0.4.0
maxulysse Nov 4, 2025
0771605
[automated] Update CHANGELOG.md
nf-core-bot Nov 4, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@

### Template

- simplify TEMPLATE with nf-core-utils 0.4.0 ([#3870](https://github.com/nf-core/tools/pull/3870))

### Linting

### Modules
Expand Down
3 changes: 2 additions & 1 deletion nf_core/pipeline-template/nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -321,7 +321,8 @@ manifest {
{% if nf_schema -%}
// Nextflow plugins
plugins {
id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
id 'nf-core-utils@0.4.0' // Helper functions for pipeline
}

validation {
Expand Down
36 changes: 10 additions & 26 deletions nf_core/pipeline-template/workflows/pipeline.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ include { MULTIQC } from '../modules/nf-core/multiqc/main'{% endi
include { paramsSummaryMap } from 'plugin/nf-schema'{% endif %}
{%- if multiqc %}
include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
Copy link
Member

@ewels ewels Nov 4, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I guess you're not deleting this in the PR here because it needs to be removed upstream and then updated? Is there a corresponding PR in nf-core/modules?

Copy link
Member Author

@maxulysse maxulysse Nov 5, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Actually my end goal is to totally remove the need for all utils subworklows and use the nf-core-utils plugin instead.
So no plan to remove from the modules yet, I think I will just let it die there

Copy link
Member Author

@maxulysse maxulysse Nov 5, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

But there should be a separate PR here to actually change the paramsSummaryMultiqc function from the subworkflow to the plugin, and so on...

include { softwareVersionsToYAML } from 'plugin/nf-core-utils'
{%- if citations or multiqc %}
include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
{%- endif %}
Expand Down Expand Up @@ -50,31 +50,15 @@ workflow {{ short_name|upper }} {
//
// Collate and save software versions
//
def topic_versions = Channel.topic("versions")
.distinct()
.branch { entry ->
versions_file: entry instanceof Path
versions_tuple: true
}

def topic_versions_string = topic_versions.versions_tuple
.map { process, tool, version ->
[ process[process.lastIndexOf(':')+1..-1], " ${tool}: ${version}" ]
}
.groupTuple(by:0)
.map { process, tool_versions ->
tool_versions.unique().sort()
"${process}:\n${tool_versions.join('\n')}"
}

softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
.mix(topic_versions_string)
.collectFile(
storeDir: "${params.outdir}/pipeline_info",
name: {% if is_nfcore %}'nf_core_' + {% endif %} '{{ short_name }}_software_' {% if multiqc %} + 'mqc_' {% endif %} + 'versions.yml',
sort: true,
newLine: true
).set { ch_collated_versions }
softwareVersionsToYAML(
softwareVersions: ch_versions.mix(channel.topic("versions")),
nextflowVersion: workflow.nextflow.version
).collectFile(
storeDir: "${params.outdir}/pipeline_info",
name: {% if is_nfcore %}'nf_core_' + {% endif %} '{{ short_name }}_software_' {% if multiqc %} + 'mqc_' {% endif %} + 'versions.yml',
sort: true,
newLine: true,
).set { ch_collated_versions }

{% if multiqc %}
//
Expand Down