Skip to content

chore(modules): migrate abricate/run to new version output format #10264

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
maxcumminsandfred-lab wants to merge 5 commits into
base: master
Choose a base branch
from
+65 −38
Open

chore(modules): migrate abricate/run to new version output format #10264

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
bb43141
chore(modules): migrate abricate/run to new version output format
Feb 25, 2026
ffb4e94
Merge branch 'master' into migrate-versions-abricate-run
maxcumminsandfred-lab Feb 25, 2026
8f212e5
fix: remove trailing whitespace
Feb 25, 2026
7ec98b8
Update meta.yml
maxcumminsandfred-lab Feb 25, 2026
bbf980b
Fix output tuple formatting in main.nf
maxcumminsandfred-lab Feb 26, 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
15 changes: 5 additions & 10 deletions modules/nf-core/abricate/run/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,10 @@ process ABRICATE_RUN {
path databasedir

output:
tuple val(meta), path("*.txt"), emit: report
path "versions.yml" , emit: versions
tuple val(meta), path("*.txt"), emit: report
tuple val("${task.process}"), val('abricate'), eval("abricate --version 2>&1 | sed 's/^.*abricate //' "), emit: versions_abricate, topic: versions


when:
task.ext.when == null || task.ext.when

Expand All @@ -36,20 +37,14 @@ process ABRICATE_RUN {
--threads ${task.cpus} \\
> ${prefix}.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
END_VERSIONS

"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
END_VERSIONS

"""
}
36 changes: 26 additions & 10 deletions modules/nf-core/abricate/run/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
name: abricate_run
description: Screen assemblies for antimicrobial resistance against multiple databases
description: Screen assemblies for antimicrobial resistance against multiple
databases
keywords:
- bacteria
- assembly
Expand Down Expand Up @@ -28,8 +29,8 @@ input:
- edam: "http://edamontology.org/format_2204" # EMBL format
- databasedir:
type: directory
description: Optional location of local copy of database files, possibly with
custom databases set up with `abricate --setupdb`
description: Optional location of local copy of database files, possibly
with custom databases set up with `abricate --setupdb`
pattern: "*/"
output:
report:
Expand All @@ -43,15 +44,30 @@ output:
description: Tab-delimited report of results
pattern: "*.{txt}"
ontologies:
- edam: "http://edamontology.org/format_2330" # Textual format
- edam: "http://edamontology.org/format_2330"
versions_abricate:
- - ${task.process}:
type: string
description: The process the versions were collected from
- abricate:
type: string
description: The tool name
- "echo \\$(abricate --version 2>&1) | sed 's/^.*abricate //' ":
type: eval
description: The expression to obtain the version of the tool
topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: "http://edamontology.org/format_3750" # YAML
- - ${task.process}:
type: string
description: The process the versions were collected from
- abricate:
type: string
description: The tool name
- "echo \\$(abricate --version 2>&1) | sed 's/^.*abricate //' ":
type: eval
description: The expression to obtain the version of the tool
authors:
- "@rpetit3"
- "@maxcumminsandfred"
maintainers:
- "@rpetit3"
52 changes: 34 additions & 18 deletions modules/nf-core/abricate/run/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,13 @@
"content": [
{
"0": [
[
"ABRICATE_RUN",
"abricate",
"1.0.1"
]
],
"1": [
[
{
"id": "test",
Expand All @@ -11,9 +18,6 @@
"test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,2204fb00277c287f5f3d82e28964aa03"
],
"report": [
[
{
Expand All @@ -23,21 +27,32 @@
"test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,2204fb00277c287f5f3d82e28964aa03"
"versions_abricate": [
[
"ABRICATE_RUN",
"abricate",
"1.0.1"
]
]
}
],
"timestamp": "2026-02-25T20:44:03.314874",
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-19T21:06:27.483697023"
"nf-test": "0.9.4",
"nextflow": "25.10.2"
}
},
"bacteroides_fragilis - genome.fa.gz": {
"content": [
{
"0": [
[
"ABRICATE_RUN",
"abricate",
"1.0.1"
]
],
"1": [
[
{
"id": "test",
Expand All @@ -46,9 +61,6 @@
"test.txt:md5,b48f4f5f78982a221038fd9f0a3aa504"
]
],
"1": [
"versions.yml:md5,2204fb00277c287f5f3d82e28964aa03"
],
"report": [
[
{
Expand All @@ -58,15 +70,19 @@
"test.txt:md5,b48f4f5f78982a221038fd9f0a3aa504"
]
],
"versions": [
"versions.yml:md5,2204fb00277c287f5f3d82e28964aa03"
"versions_abricate": [
[
"ABRICATE_RUN",
"abricate",
"1.0.1"
]
]
}
],
"timestamp": "2026-02-25T20:43:54.223267",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-05-23T12:30:00.97526706"
"nf-test": "0.9.4",
"nextflow": "25.10.2"
}
}
}