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Migrate hlala to topic channels and bump version #11282

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b90128b
Migrate hlala/preparegraph and hlala/typing to topic channels
jonasscheid Apr 23, 2026
6cddfc1
Restore quay.io/ prefix on container specification
jonasscheid Apr 23, 2026
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12 changes: 1 addition & 11 deletions modules/nf-core/hlala/preparegraph/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ process HLALA_PREPAREGRAPH {

output:
tuple val(meta), path("${graph}") , emit: graph
path "versions.yml", emit: versions
tuple val("${task.process}"), val('hla-la'), eval('echo 1.0.4'), emit: versions_hlala, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -30,11 +30,6 @@ process HLALA_PREPAREGRAPH {
${bin} \\
--action prepareGraph \\
--PRG_graph_dir $graph

cat <<-END_VERSIONS > versions.yml
"${task.process}":
hlala: 1.0.3
END_VERSIONS
"""

stub:
Expand Down Expand Up @@ -76,10 +71,5 @@ process HLALA_PREPAREGRAPH {
touch ${graph}/PRG/graph.txt
touch ${graph}/PRG/segments.txt
touch ${graph}/PRG/positions.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
hlala: 1.0.3
END_VERSIONS
"""
}
26 changes: 20 additions & 6 deletions modules/nf-core/hlala/preparegraph/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -33,13 +33,27 @@ output:
- ${graph}:
type: directory
description: PRG graph directory
versions_hlala:
- - ${task.process}:
type: string
description: The process the versions were collected from
- hla-la:
type: string
description: The name of the tool
- echo 1.0.4:
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
- hla-la:
type: string
description: The name of the tool
- echo 1.0.4:
type: eval
description: The expression to obtain the version of the tool
authors:
- "@mapo9"
maintainers:
Expand Down
28 changes: 17 additions & 11 deletions modules/nf-core/hlala/preparegraph/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,11 @@
]
],
"1": [
"versions.yml:md5,9c44ff8e47df418f82531b71b9613945"
[
"HLALA_PREPAREGRAPH",
"hla-la",
"1.0.4"
]
],
"graph": [
[
Expand Down Expand Up @@ -115,16 +119,20 @@
]
]
],
"versions": [
"versions.yml:md5,9c44ff8e47df418f82531b71b9613945"
"versions_hlala": [
[
"HLALA_PREPAREGRAPH",
"hla-la",
"1.0.4"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2025-03-26T10:50:19.125173"
"timestamp": "2026-04-23T20:25:20.521118567"
},
"homo_sapiens - prg": {
"content": [
Expand Down Expand Up @@ -170,7 +178,6 @@
"hlala/PRG_test/serializedGRAPH_preGapPathIndex",
"hlala/PRG_test/translation",
"hlala/PRG_test/translation/100.txt",
"hlala/versions.yml",
"unzip",
"unzip/test",
"unzip/test/PRG_test",
Expand Down Expand Up @@ -236,7 +243,6 @@
"serializedGRAPH:md5,a88016a601377a967feb04c1bbeeba65",
"serializedGRAPH_preGapPathIndex:md5,65ea9cd52a00ffd51a2460c6887b277e",
"100.txt:md5,8dd91725d9a2f1f71a82ae1d190aa840",
"versions.yml:md5,f1108f072a11ccc5a063bf17a78ecd2d",
".nextflow.log:md5,f22b6ca679424bea221fe100b4162b4a",
"100_gene_HLA-A_9_exon_5.txt:md5,fa4f97441bdd999f3ada1a49e67b726b",
"100_gene_HLA-A_9_exon_5.txt.graph:md5,0c5532614ffa94e30321c521e5a5046e",
Expand All @@ -261,9 +267,9 @@
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2025-03-26T10:50:11.256875"
"timestamp": "2026-04-23T20:24:57.389656201"
}
}
17 changes: 2 additions & 15 deletions modules/nf-core/hlala/typing/main.nf
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Expand Up @@ -21,15 +21,14 @@ process HLALA_TYPING {
tuple val(meta), path("results/reads_per_level.txt") , emit: reads_per_level
tuple val(meta), path("results/remapped_with_a.bam") , emit: remapped
tuple val(meta), path("results/remapped_with_a.bam.bai") , emit: remapped_index
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('hla-la'), eval('echo 1.0.4'), emit: versions_hlala, topic: versions

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

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

def bin = ""
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
Expand All @@ -47,17 +46,10 @@ process HLALA_TYPING {
--maxThreads $task.cpus \\
$args

mkdir -p results
mv ${prefix}/ results/

cat <<-END_VERSIONS > versions.yml
"${task.process}":
hla-la: ${VERSION}
END_VERSIONS
mv ${prefix} results
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@FriederikeHanssen FriederikeHanssen Apr 24, 2026

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ideally we should avoid this. on cloud compute this produces a real copy of the data and not just renames it. but maybe for a different PR as I see it is a pre-existing condition.

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@FriederikeHanssen FriederikeHanssen Apr 24, 2026

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https://youtu.be/MX_95p9YOts?si=18go-_uCkBheo46Q

"""

stub:
def VERSION = '1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
mkdir -p results

Expand Down Expand Up @@ -146,10 +138,5 @@ process HLALA_TYPING {
touch results/hla/R1_readIDs_K.txt
touch results/hla/R1_readIDs_V.txt
touch results/hla/summaryStatistics.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
hla-la: ${VERSION}
END_VERSIONS
"""
}
26 changes: 20 additions & 6 deletions modules/nf-core/hlala/typing/meta.yml
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Expand Up @@ -144,13 +144,27 @@ output:
description: Remapped BAM index file
pattern: "*.bam.bai"
ontologies: []
versions_hlala:
- - ${task.process}:
type: string
description: The process the versions were collected from
- hla-la:
type: string
description: The name of the tool
- echo 1.0.4:
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
- hla-la:
type: string
description: The name of the tool
- echo 1.0.4:
type: eval
description: The expression to obtain the version of the tool
authors:
- "@mapo9"
maintainers:
Expand Down
5 changes: 1 addition & 4 deletions modules/nf-core/hlala/typing/tests/main.nf.test
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Expand Up @@ -99,10 +99,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(process.out).match() }
)
}
}
Expand Down
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