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Migration to topics channels: diamond/blastp #10766 #10885

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0676624
module update version
LorenzoCampanelli1102 Mar 12, 2026
4e079e5
modules versions update
LorenzoCampanelli1102 Mar 13, 2026
189af43
fixed/version diamond
LorenzoCampanelli1102 Mar 13, 2026
0117d08
Merge branch 'master' into module_diamond_blastp
LorenzoCampanelli1102 Mar 13, 2026
1d46ed8
Merge branch 'master' into module_diamond_blastp
LorenzoCampanelli1102 Mar 13, 2026
bb15d25
Merge branch 'master' into module_diamond_blastp
atrigila Mar 13, 2026
3fb500a
Merge branch 'master' into module_diamond_blastp
LorenzoCampanelli1102 Mar 13, 2026
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2 changes: 1 addition & 1 deletion modules/nf-core/diamond/blastp/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ process DIAMOND_BLASTP {
tuple val(meta), path('*.{sam,sam.gz}'), optional: true, emit: sam
tuple val(meta), path('*.{tsv,tsv.gz}'), optional: true, emit: tsv
tuple val(meta), path('*.{paf,paf.gz}'), optional: true, emit: paf
tuple val("${task.process}"), val('diamond'), eval('diamond --version 2>&1 | tail -n 1 | sed "s/^diamond version //"'), emit: versions_diamond, topic: versions
tuple val("${task.process}"), val('diamond'), eval("diamond --version 2>&1 | sed 's/diamond version //g'"), emit: versions_diamond, topic: versions

when:
task.ext.when == null || task.ext.when
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6 changes: 3 additions & 3 deletions modules/nf-core/diamond/blastp/meta.yml
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Expand Up @@ -26,7 +26,7 @@ input:
description: Input fasta file containing query sequences
pattern: "*.{fa,fasta,fa.gz,fasta.gz}"
ontologies:
- edam: http://edamontology.org/format_1929 # FASTA
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@atrigila atrigila Mar 13, 2026

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Keep the comment

- edam: http://edamontology.org/format_1929
- - meta2:
type: map
description: |
Expand Down Expand Up @@ -148,7 +148,7 @@ output:
- diamond:
type: string
description: The name of the tool
- diamond --version 2>&1 | tail -n 1 | sed "s/^diamond version //":
- diamond --version 2>&1 | sed 's/diamond version //g':
type: eval
description: The expression to obtain the version of the tool
topics:
Expand All @@ -159,7 +159,7 @@ topics:
- diamond:
type: string
description: The name of the tool
- diamond --version 2>&1 | tail -n 1 | sed "s/^diamond version //":
- diamond --version 2>&1 | sed 's/diamond version //g':
type: eval
description: The expression to obtain the version of the tool
authors:
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2 changes: 1 addition & 1 deletion modules/nf-core/diamond/blastp/tests/main.nf.test
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Expand Up @@ -84,7 +84,7 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert process.out.daa },
{ assert snapshot(process.out.versions).match("daa") }
{ assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match("daa")}
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@atrigila atrigila Mar 13, 2026

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Remove the match.daa

Your error says: "snapshot with id 'daa' not found."

Remove it and re-do the snapshots.

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@atrigila atrigila Mar 13, 2026

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Keep this: { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }

)
}

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151 changes: 5 additions & 146 deletions modules/nf-core/diamond/blastp/tests/main.nf.test.snap
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Expand Up @@ -72,7 +72,7 @@
]
}
],
"timestamp": "2026-03-10T18:29:43.631582451",
"timestamp": "2026-03-13T16:05:50.64340715",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
Expand Down Expand Up @@ -151,7 +151,7 @@
]
}
],
"timestamp": "2026-03-10T18:30:12.968864721",
"timestamp": "2026-03-13T16:06:14.810071467",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
Expand Down Expand Up @@ -230,7 +230,7 @@
]
}
],
"timestamp": "2026-03-10T18:29:53.37630928",
"timestamp": "2026-03-13T16:05:59.005111568",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
Expand All @@ -239,157 +239,16 @@
"sarscov2 - proteome - double fasta/double db input": {
"content": [
{
"0": [

],
"1": [

],
"2": [
[
{
"id": "fasta1",
"db": "db1"
},
"fasta1.db1.txt:md5,2515cf88590afa32356497e79a51fce9"
],
[
{
"id": "fasta1",
"db": "db2"
},
"fasta1.db2.txt:md5,8b41a8752379f7bd8722258962c598a4"
],
[
{
"id": "fasta2",
"db": "db1"
},
"fasta2.db1.txt:md5,3be947b0e6c69c59491f817b03b1256f"
],
[
{
"id": "fasta2",
"db": "db2"
},
"fasta2.db2.txt:md5,f2461bcecbf4f87cefe952179505aa8f"
]
Comment on lines -242 to -276
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@atrigila atrigila Mar 13, 2026

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Everything here seems to be deleted. You need to update the snapshots or check why these changed.

],
"3": [

],
"4": [

],
"5": [

],
"6": [

],
"7": [
[
"DIAMOND_BLASTP",
"diamond",
"2.1.23"
],
[
"DIAMOND_BLASTP",
"diamond",
"2.1.23"
],
[
"DIAMOND_BLASTP",
"diamond",
"2.1.23"
],
[
"DIAMOND_BLASTP",
"diamond",
"2.1.23"
]
],
"blast": [

],
"daa": [

],
"paf": [

],
"sam": [

],
"tsv": [

],
"txt": [
[
{
"id": "fasta1",
"db": "db1"
},
"fasta1.db1.txt:md5,2515cf88590afa32356497e79a51fce9"
],
[
{
"id": "fasta1",
"db": "db2"
},
"fasta1.db2.txt:md5,8b41a8752379f7bd8722258962c598a4"
],
[
{
"id": "fasta2",
"db": "db1"
},
"fasta2.db1.txt:md5,3be947b0e6c69c59491f817b03b1256f"
],
[
{
"id": "fasta2",
"db": "db2"
},
"fasta2.db2.txt:md5,f2461bcecbf4f87cefe952179505aa8f"
]
],
"versions_diamond": [
[
"DIAMOND_BLASTP",
"diamond",
"2.1.23"
],
[
"DIAMOND_BLASTP",
"diamond",
"2.1.23"
],
[
"DIAMOND_BLASTP",
"diamond",
"2.1.23"
],
[
"DIAMOND_BLASTP",
"diamond",
"2.1.23"
]
],
"xml": [

]
}
],
"timestamp": "2026-03-10T18:30:23.940020081",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
},
"daa": {
"content": null,
"timestamp": "2026-03-10T18:30:03.067997422",
"timestamp": "2026-03-13T16:06:06.927716521",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
Expand Down Expand Up @@ -468,7 +327,7 @@
]
}
],
"timestamp": "2026-03-10T18:30:33.408520524",
"timestamp": "2026-03-13T16:06:22.991148135",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
Expand Down
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