Skip to content

Migrate universc versions topic #12479

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
atrigila wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Migrate universc versions topic #12479

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
4549f2d
chore: migrate universc versions topic
atrigila Jul 31, 2026
311660a
Merge branch 'master' into migrate-topics-universc
atrigila Jul 31, 2026
461e4e0
Merge branch 'master' into migrate-topics-universc
SPPearce Aug 3, 2026
c7cd9eb
Merge branch 'master' into migrate-topics-universc
SPPearce Aug 14, 2026
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
27 changes: 8 additions & 19 deletions modules/nf-core/universc/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,8 @@ process UNIVERSC {

output:
tuple val(meta), path("${prefix}/outs/*"), emit: outs
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('cellranger'), eval('cellranger count --version 2>&1 | head -n 2 | tail -n 1 | sed "s/^.* //g" | sed "s/(//g" | sed "s/)//g"'), emit: versions_cellranger, topic: versions
tuple val("${task.process}"), val('universc'), eval('bash /universc/launch_universc.sh --version | grep version | grep universc | sed "s/^.* //g"'), emit: versions_universc, topic: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -47,12 +48,6 @@ process UNIVERSC {
echo !! > ${prefix}/outs/_invocation
cp _log ${prefix}/outs/_log
cp _err ${prefix}/outs/_err

cat <<-END_VERSIONS > versions.yml
"${task.process}":
cellranger: \$(echo \$(cellranger count --version 2>&1 | head -n 2 | tail -n 1 | sed 's/^.* //g' | sed 's/(//g' | sed 's/)//g' ))
universc: \$(echo \$(bash /universc/launch_universc.sh --version | grep version | grep universc | sed 's/^.* //g' ))
END_VERSIONS
"""


Expand Down Expand Up @@ -81,22 +76,16 @@ process UNIVERSC {

mkdir -p filtered_feature_bc_matrix
touch filtered_feature_bc_matrix.h5
echo | gzip > filtered_feature_bc_matrix/barcodes.tsv.gz
echo | gzip > filtered_feature_bc_matrix/features.tsv.gz
echo | gzip > filtered_feature_bc_matrix/matrix.mtx.gz
echo "" | gzip > filtered_feature_bc_matrix/barcodes.tsv.gz
echo "" | gzip > filtered_feature_bc_matrix/features.tsv.gz
echo "" | gzip > filtered_feature_bc_matrix/matrix.mtx.gz

mkdir -p raw_feature_bc_matrix
touch raw_feature_bc_matrix.h5
echo | gzip > raw_feature_bc_matrix/barcodes.tsv.gz
echo | gzip > raw_feature_bc_matrix/features.tsv.gz
echo | gzip > raw_feature_bc_matrix/matrix.mtx.gz
echo "" | gzip > raw_feature_bc_matrix/barcodes.tsv.gz
echo "" | gzip > raw_feature_bc_matrix/features.tsv.gz
echo "" | gzip > raw_feature_bc_matrix/matrix.mtx.gz

cd ../..

cat <<-END_VERSIONS > versions.yml
"${task.process}":
cellranger: \$(echo \$(cellranger count --version 2>&1 | head -n 2 | tail -n 1 | sed 's/^.* //g' | sed 's/(//g' | sed 's/)//g' ))
universc: \$(echo \$(bash /universc/launch_universc.sh --version | grep version | grep universc | sed 's/^.* //g' ))
END_VERSIONS
"""
}
45 changes: 39 additions & 6 deletions modules/nf-core/universc/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,13 +54,46 @@ output:
description: Files containing the outputs of Cell Ranger
pattern: "${prefix}/outs/*"
ontologies: []
versions_cellranger:
- - ${task.process}:
type: string
description: The name of the process
- cellranger:
type: string
description: The name of the tool
- 'cellranger count --version 2>&1 | head -n 2 | tail -n 1 | sed "s/^.* //g" | sed "s/(//g" | sed "s/)//g"':
type: eval
description: The expression to obtain the version of the tool
versions_universc:
- - ${task.process}:
type: string
description: The name of the process
- universc:
type: string
description: The name of the tool
- 'bash /universc/launch_universc.sh --version | grep version | grep universc | sed "s/^.* //g"':
type: eval
description: The expression to obtain the version of the tool
topics:
versions:
- versions.yml:
type: file
description: File containing software version
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The name of the process
- cellranger:
type: string
description: The name of the tool
- 'cellranger count --version 2>&1 | head -n 2 | tail -n 1 | sed "s/^.* //g" | sed "s/(//g" | sed "s/)//g"':
type: eval
description: The expression to obtain the version of the tool
- - ${task.process}:
type: string
description: The name of the process
- universc:
type: string
description: The name of the tool
- 'bash /universc/launch_universc.sh --version | grep version | grep universc | sed "s/^.* //g"':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@kbattenb"
- "@tomkellygenetics"
Expand Down
13 changes: 2 additions & 11 deletions modules/nf-core/universc/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,13 +45,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.outs[0][1].collect{
file(it).name.find(/_err|_log|\.h5|\.bam/)
? file(it).name : it // _err is empty and others are not stable
},
process.out.versions
).match() }
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ['outs'])).match() }
)
}
}
Expand Down Expand Up @@ -80,10 +74,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
126 changes: 55 additions & 71 deletions modules/nf-core/universc/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"universc_10x -- stub": {
"content": [
{
"0": [
"outs": [
[
{
"id": "test",
Expand Down Expand Up @@ -33,90 +33,74 @@
]
]
],
"1": [
"versions.yml:md5,70bfcfea05b26a198a980e8b0eabb348"
"versions_cellranger": [
[
"UNIVERSC",
"cellranger",
"3.0.2.9001"
]
],
"versions_universc": [
[
"UNIVERSC",
"universc",
"1.2.5.1"
]
]
}
],
"timestamp": "2026-07-31T17:17:10.433427325",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"universc_10x": {
"content": [
{
"outs": [
[
{
"id": "test",
"single_end": false
},
[
"_err:md5,d41d8cd98f00b204e9800998ecf8427e",
"_invocation:md5,d41d8cd98f00b204e9800998ecf8427e",
"_log:md5,d41d8cd98f00b204e9800998ecf8427e",
"basic_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"barcodes.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"features.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"matrix.mtx.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
],
"filtered_feature_bc_matrix.h5:md5,d41d8cd98f00b204e9800998ecf8427e",
"metrics_summary.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
"molecule_info.h5:md5,d41d8cd98f00b204e9800998ecf8427e",
"possorted_genome_bam.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
"possorted_genome_bam.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"barcodes.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"features.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"matrix.mtx.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
],
"raw_feature_bc_matrix.h5:md5,d41d8cd98f00b204e9800998ecf8427e",
"web_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e"
"_err",
"_invocation",
"_log",
"basic_stats.txt",
"filtered_feature_bc_matrix",
"filtered_feature_bc_matrix.h5",
"metrics_summary.csv",
"molecule_info.h5",
"possorted_genome_bam.bam",
"possorted_genome_bam.bam.bai",
"raw_feature_bc_matrix",
"raw_feature_bc_matrix.h5",
"web_summary.html"
]
]
],
"versions": [
"versions.yml:md5,70bfcfea05b26a198a980e8b0eabb348"
"versions_cellranger": [
[
"UNIVERSC",
"cellranger",
"3.0.2.9001"
]
],
"versions_universc": [
[
"UNIVERSC",
"universc",
"1.2.5.1"
]
]
},
{
"UNIVERSC": {
"cellranger": "3.0.2.9001",
"universc": "1.2.5.1"
}
}
],
"timestamp": "2026-07-31T17:17:03.350245092",
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.2"
},
"timestamp": "2025-05-29T12:54:18.627245737"
},
"universc_10x": {
"content": [
[
"_err",
"_invocation:md5,adbbbc1027756be9fdeebabf979863e5",
"_log",
"basic_stats.txt:md5,90004df04ec7b65a0dd8d26a08e55fd2",
[
"barcodes.tsv.gz:md5,11504585bad0cefa736757ed934b5417",
"features.tsv.gz:md5,7f05863a60b0ef33073ca1833f27c497",
"matrix.mtx.gz:md5,429de6faa1dc870ca64f0150b2ad7a76"
],
"filtered_feature_bc_matrix.h5",
"metrics_summary.csv:md5,bba1b122b15698d97a034af61e3fcd59",
"molecule_info.h5",
"possorted_genome_bam.bam",
"possorted_genome_bam.bam.bai",
[
"barcodes.tsv.gz:md5,bf994f994561412303520a2fb3ac87f8",
"features.tsv.gz:md5,7f05863a60b0ef33073ca1833f27c497",
"matrix.mtx.gz:md5,476dac7e51140291ad7e3219b8c7cc1a"
],
"raw_feature_bc_matrix.h5",
"web_summary.html:md5,98a001e1278b03322211f59a48eb8bb2"
],
[
"versions.yml:md5,70bfcfea05b26a198a980e8b0eabb348"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.2"
},
"timestamp": "2025-05-29T13:33:37.644843156"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
}
}
Loading