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Update to use records and topic channel #44

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5ce64e4
Update to use records and topic channel
markquintontulloch Sep 29, 2026
9fb261a
Bump genomio version
markquintontulloch Sep 30, 2026
a60af94
Revert to correct Genomio version and update snapshots
markquintontulloch Sep 30, 2026
e894b25
Remove task.process from topic tuples
markquintontulloch Sep 30, 2026
b8ead5e
Reinstate task.process in versions topic tuple for compatability with…
markquintontulloch Sep 30, 2026
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10 changes: 7 additions & 3 deletions modules/ensembl/fasta/recombine/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@
// See the License for the specific language governing permissions and
// limitations under the License.

nextflow.enable.types = true

process FASTA_RECOMBINE {

tag "${meta.id}"
Expand All @@ -22,11 +24,13 @@ process FASTA_RECOMBINE {
container "docker.io/ensemblorg/ensembl-genomio:v1.7.0"

input:
tuple val(meta), path(fasta_manifest), path(agp)
record(meta: Map, fasta_manifest: Path, agp: Path?)

output:
tuple val(meta), path("${meta.id}.fa"), emit: recombined_fasta
tuple val("${task.process}"), val('fasta_recombine'), eval("fasta_recombine --version"), emit: versions_fasta_recombine, topic: versions
record(meta: meta, recombined_fasta: file("${meta.id}.fa"))

topic:
tuple(task.process, 'fasta_recombine', eval("fasta_recombine --version 2>/dev/null || echo unknown")) >> 'versions'

when:
task.ext.when == null || task.ext.when
Expand Down
12 changes: 1 addition & 11 deletions modules/ensembl/fasta/recombine/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -46,16 +46,6 @@ output:
pattern: "*.fa"
ontologies:
- edam: http://edamontology.org/format_1929 # FASTA
versions_fasta_recombine:
- - ${task.process}:
type: string
description: The name of the process.
- fasta_recombine:
type: string
description: The name of the tool.
- "fasta_recombine --version":
type: eval
description: The expression to obtain the version of the tool
topics:
versions:
- - ${task.process}:
Expand All @@ -64,7 +54,7 @@ topics:
- fasta_recombine:
type: string
description: The name of the tool.
- "fasta_recombine --version":
- "fasta_recombine --version 2>/dev/null || echo unknown":
type: eval
description: The expression to obtain the version of the tool
authors:
Expand Down
25 changes: 13 additions & 12 deletions modules/ensembl/fasta/recombine/tests/main.nf.test
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Expand Up @@ -24,6 +24,7 @@ nextflow_process {
tag "modules_ensembl"
tag "fasta"
tag "fasta/recombine"
topics "versions"

test("stub outputs: header mode") {

Expand All @@ -38,18 +39,18 @@ nextflow_process {
def no_file = file("NO_FILE")
no_file.text = ""

input[0] = [
[ id: 'test' ],
manifest,
no_file
]
input[0] = record(meta: [ id: 'test' ], fasta_manifest: manifest, agp: no_file)
"""
}
}

then {
assert process.trace.tasks().size() == 1
assert process.out.recombined_fasta.size() == 1
assert process.out[0].size() == 1
assert file(process.out[0][0].recombined_fasta).name == 'test.fa'
assert topics.versions.size() == 1
assert topics.versions[0].size() == 3
assert topics.versions[0][0] == 'FASTA_RECOMBINE'
assert process.success
assert snapshot(process.out).match()
}
Expand All @@ -67,18 +68,18 @@ nextflow_process {

def agp = file("test.agp")
agp.text = ""
input[0] = [
[ id: 'test' ],
manifest,
agp
]
input[0] = record(meta: [ id: 'test' ], fasta_manifest: manifest, agp: agp)
"""
}
}

then {
assert process.trace.tasks().size() == 1
assert process.out.recombined_fasta.size() == 1
assert process.out[0].size() == 1
assert file(process.out[0][0].recombined_fasta).name == 'test.fa'
assert topics.versions.size() == 1
assert topics.versions[0].size() == 3
assert topics.versions[0][0] == 'FASTA_RECOMBINE'
assert process.success
assert snapshot(process.out).match()
}
Expand Down
72 changes: 14 additions & 58 deletions modules/ensembl/fasta/recombine/tests/main.nf.test.snap
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Expand Up @@ -3,82 +3,38 @@
"content": [
{
"0": [
[
{
{
"meta": {
"id": "test"
},
"test.fa:md5,c40116e7d725da4662e6bdd654f70075"
]
],
"1": [
[
"FASTA_RECOMBINE",
"fasta_recombine",
"1.7.0"
]
],
"recombined_fasta": [
[
{
"id": "test"
},
"test.fa:md5,c40116e7d725da4662e6bdd654f70075"
]
],
"versions_fasta_recombine": [
[
"FASTA_RECOMBINE",
"fasta_recombine",
"1.7.0"
]
"recombined_fasta": "test.fa:md5,c40116e7d725da4662e6bdd654f70075"
}
]
}
],
"timestamp": "2026-06-11T18:08:46.722339",
"timestamp": "2026-09-29T12:53:47.242818",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.3"
"nf-test": "0.9.5",
"nextflow": "26.04.3"
}
},
"stub outputs: header mode": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.fa:md5,c40116e7d725da4662e6bdd654f70075"
]
],
"1": [
[
"FASTA_RECOMBINE",
"fasta_recombine",
"1.7.0"
]
],
"recombined_fasta": [
[
{
{
"meta": {
"id": "test"
},
"test.fa:md5,c40116e7d725da4662e6bdd654f70075"
]
],
"versions_fasta_recombine": [
[
"FASTA_RECOMBINE",
"fasta_recombine",
"1.7.0"
]
"recombined_fasta": "test.fa:md5,c40116e7d725da4662e6bdd654f70075"
}
]
}
],
"timestamp": "2026-06-11T18:08:44.434921",
"timestamp": "2026-09-29T12:53:44.690151",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.3"
"nf-test": "0.9.5",
"nextflow": "26.04.3"
}
}
}
15 changes: 11 additions & 4 deletions modules/ensembl/fasta/split/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@
// See the License for the specific language governing permissions and
// limitations under the License.

nextflow.enable.types = true

process FASTA_SPLIT {
tag "${meta.id}"
label 'process_medium'
Expand All @@ -21,12 +23,17 @@ process FASTA_SPLIT {
container "docker.io/ensemblorg/ensembl-genomio:v1.7.0"

input:
tuple val(meta), path(fasta), val(longest_seq_bp)
record(meta: Map, fasta: Path, longest_seq_bp: Integer)

output:
tuple val(meta), path("splits/**/*.fa"), emit: fastas
tuple val(meta), path("splits/*.agp"), emit: agp, optional: true
tuple val("${task.process}"), val('fasta_split'), eval("fasta_split --version"), emit: versions_fasta_split, topic: versions
record(
meta: meta,
fastas: files("splits/**/*.fa"),
agp: file("splits/*.agp", optional: true)
)

topic:
tuple(task.process, 'fasta_split', eval("fasta_split --version 2>/dev/null || echo unknown")) >> 'versions'

when:
task.ext.when == null || task.ext.when
Expand Down
12 changes: 1 addition & 11 deletions modules/ensembl/fasta/split/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -55,16 +55,6 @@ output:
pattern: "splits/*.agp"
ontologies:
- edam: "http://edamontology.org/format_3693" # AGP
versions_fasta_split:
- - ${task.process}:
type: string
description: The name of the process.
- fasta_split:
type: string
description: The name of the tool.
- "fasta_split --version":
type: eval
description: The expression to obtain the version of the tool
topics:
versions:
- - ${task.process}:
Expand All @@ -73,7 +63,7 @@ topics:
- fasta_split:
type: string
description: The name of the tool.
- "fasta_split --version":
- "fasta_split --version 2>/dev/null || echo unknown":
type: eval
description: The expression to obtain the version of the tool
authors:
Expand Down
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