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Update to topics hmmer/* #11637

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e7643ae
Update to topics
LouisLeNezet May 12, 2026
c8e561e
Update tests
LouisLeNezet May 12, 2026
f865100
Fix meta
LouisLeNezet May 12, 2026
851ed1c
Apply suggestions from code review
LouisLeNezet May 13, 2026
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2 changes: 1 addition & 1 deletion modules/nf-core/hmmer/eslalimask/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::hmmer=3.3.2
- bioconda::hmmer=3.4
17 changes: 4 additions & 13 deletions modules/nf-core/hmmer/eslalimask/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process HMMER_ESLALIMASK {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1':
'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }"
'https://depot.galaxyproject.org/singularity/hmmer:3.4--hb6cb901_4' :
'quay.io/biocontainers/hmmer:3.4--hb6cb901_4' }"

input:
tuple val(meta), path(unmaskedaln), val(fmask_rf), val(fmask_all), val(gmask_rf), val(gmask_all), val(pmask_rf), val(pmask_all)
Expand All @@ -19,7 +19,8 @@ process HMMER_ESLALIMASK {
path "*.gmask-all.gz" , emit: gmask_all, optional: true
path "*.pmask-rf.gz" , emit: pmask_rf , optional: true
path "*.pmask-all.gz" , emit: pmask_all, optional: true
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('hmmer'), eval("hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'"), emit: versions_hmmer, topic: versions
tuple val("${task.process}"), val('easel'), eval("esl-alimask -h | sed '2!d;s/^# Easel *//;s/ .*//'"), emit: versions_easel, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -45,11 +46,6 @@ process HMMER_ESLALIMASK {
$args $unmaskedaln $maskfile

gzip ${prefix}.*mask*

cat <<-END_VERSIONS > versions.yml
"${task.process}":
hmmer/easel: \$(esl-alimask -h | grep -o '^# Easel [0-9.]*' | sed 's/^# Easel *//')
END_VERSIONS
"""

stub:
Expand All @@ -72,10 +68,5 @@ process HMMER_ESLALIMASK {
${pmask_allarg}

gzip ${prefix}.*mask*

cat <<-END_VERSIONS > versions.yml
"${task.process}":
hmmer/easel: \$(esl-alimask -h | grep -o '^# Easel [0-9.]*' | sed 's/^# Easel *//')
END_VERSIONS
"""
}
65 changes: 51 additions & 14 deletions modules/nf-core/hmmer/eslalimask/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,8 @@ tools:
homepage: http://hmmer.org/
documentation: http://hmmer.org/documentation.html
doi: "10.1371/journal.pcbi.1002195"
licence: ["BSD-3-Clause"]
licence:
- "BSD-3-Clause"
identifier: ""
input:
- - meta:
Expand All @@ -25,24 +26,27 @@ input:
ontologies: []
- fmask_rf:
type: boolean
description: Flag to output optional file with final mask of non-gap RF len
description: Flag to output optional file with final mask of non-gap RF
len
- fmask_all:
type: boolean
description: Flag to output optional file with final mask of full aln len
- gmask_rf:
type: boolean
description: Flag to output optional file gap-based 0/1 mask of non-gap RF len
description: Flag to output optional file gap-based 0/1 mask of non-gap RF
len
- gmask_all:
type: boolean
description: Flag to output optional file gap-based 0/1 mask of full aln len
description: Flag to output optional file gap-based 0/1 mask of full aln
len
- pmask_rf:
type: boolean
description: Flag to output optional file with PP-based 0/1 mask of non-gap
RF len
description: Flag to output optional file with PP-based 0/1 mask of
non-gap RF len
- pmask_all:
type: boolean
description: Flag to output optional file with PP-based 0/1 mask of full aln
len
description: Flag to output optional file with PP-based 0/1 mask of full
aln len
- maskfile:
type: file
description: mask file, see program documentation
Expand Down Expand Up @@ -103,13 +107,46 @@ output:
pattern: "*.pmask-all.gz"
ontologies:
- edam: http://edamontology.org/format_3989 # GZIP format
versions_hmmer:
- - ${task.process}:
type: string
description: The name of the process
- hmmer:
type: string
description: The name of the tool
- hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//':
type: eval
description: The expression to obtain the version of the tool
versions_easel:
- - ${task.process}:
type: string
description: The name of the process
- easel:
type: string
description: The name of the tool
- esl-alimask -h | sed '2!d;s/^# Easel *//;s/ .*//':
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 name of the process
- hmmer:
type: string
description: The name of the tool
- hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//':
type: eval
description: The expression to obtain the version of the tool
- - ${task.process}:
type: string
description: The name of the process
- easel:
type: string
description: The name of the tool
- esl-alimask -h | sed '2!d;s/^# Easel *//;s/ .*//':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@erikrikarddaniel"
maintainers:
Expand Down
13 changes: 5 additions & 8 deletions modules/nf-core/hmmer/eslalimask/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,9 @@ nextflow_process {
"""
input[0] = [
[id:'test'],
file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')
file(params.modules_testdata_base_path + 'delete_me/hmmer/e_coli_k12_16s.fna.gz')
]
input[1] = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
input[1] = file(params.modules_testdata_base_path + 'delete_me/hmmer/bac.16S_rRNA.hmm.gz')
"""
}
}
Expand All @@ -43,7 +43,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand All @@ -64,7 +64,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand All @@ -86,10 +86,7 @@ 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
161 changes: 51 additions & 110 deletions modules/nf-core/hmmer/eslalimask/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,35 +2,6 @@
"ecoli - hmm no optional output files - []": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.masked.sthlm.gz:md5,9e2d2c1f4dbe2851457b478fd75e7f69"
]
],
"1": [

],
"2": [

],
"3": [

],
"4": [

],
"5": [

],
"6": [

],
"7": [
"versions.yml:md5,499a23c59008702b0bfda72cdce1116a"
],
"fmask_all": [

],
Expand All @@ -57,49 +28,31 @@
"pmask_rf": [

],
"versions": [
"versions.yml:md5,499a23c59008702b0bfda72cdce1116a"
"versions_easel": [
[
"HMMER_ESLALIMASK",
"easel",
"0.49"
]
],
"versions_hmmer": [
[
"HMMER_ESLALIMASK",
"hmmer",
"3.4"
]
]
}
],
"timestamp": "2026-05-12T20:15:39.895105995",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-14T11:34:10.295624757"
"nf-test": "0.9.4",
"nextflow": "26.03.0"
}
},
"ecoli - hmm with optional output files - []": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.masked.sthlm.gz:md5,5313874ae46c8a913f507c507321a3d9"
]
],
"1": [
"test.fmask-rf.gz:md5,9ec8400b91b0ad4b69f91888f6762caf"
],
"2": [
"test.fmask-all.gz:md5,7da678b3d106269ef4675b575e313244"
],
"3": [
"test.gmask-rf.gz:md5,5e028068b40861990b5e8c18cb4fbb75"
],
"4": [
"test.gmask-all.gz:md5,e1a8c3410bd77bb4c27410c8ec5f35ea"
],
"5": [
"test.pmask-rf.gz:md5,9ec8400b91b0ad4b69f91888f6762caf"
],
"6": [
"test.pmask-all.gz:md5,7da678b3d106269ef4675b575e313244"
],
"7": [
"versions.yml:md5,499a23c59008702b0bfda72cdce1116a"
],
"fmask_all": [
"test.fmask-all.gz:md5,7da678b3d106269ef4675b575e313244"
],
Expand All @@ -126,49 +79,31 @@
"pmask_rf": [
"test.pmask-rf.gz:md5,9ec8400b91b0ad4b69f91888f6762caf"
],
"versions": [
"versions.yml:md5,499a23c59008702b0bfda72cdce1116a"
"versions_easel": [
[
"HMMER_ESLALIMASK",
"easel",
"0.49"
]
],
"versions_hmmer": [
[
"HMMER_ESLALIMASK",
"hmmer",
"3.4"
]
]
}
],
"timestamp": "2026-05-12T20:15:46.701235748",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-14T11:36:02.56290786"
"nf-test": "0.9.4",
"nextflow": "26.03.0"
}
},
"ecoli - hmm with optional output files - [] -- stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.masked.sthlm.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"test.fmask-rf.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"2": [
"test.fmask-all.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"3": [
"test.gmask-rf.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"4": [
"test.gmask-all.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"5": [
"test.pmask-rf.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"6": [
"test.pmask-all.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"7": [
"versions.yml:md5,499a23c59008702b0bfda72cdce1116a"
],
"fmask_all": [
"test.fmask-all.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
],
Expand All @@ -195,20 +130,26 @@
"pmask_rf": [
"test.pmask-rf.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"versions": [
"versions.yml:md5,499a23c59008702b0bfda72cdce1116a"
"versions_easel": [
[
"HMMER_ESLALIMASK",
"easel",
"0.49"
]
],
"versions_hmmer": [
[
"HMMER_ESLALIMASK",
"hmmer",
"3.4"
]
]
},
{
"HMMER_ESLALIMASK": {
"hmmer/easel": 0.48
}
}
],
"timestamp": "2026-05-12T20:15:53.604659572",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-14T11:41:05.2704503"
"nf-test": "0.9.4",
"nextflow": "26.03.0"
}
}
}
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