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Update to topics hostile/* #11748

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70a0b95
Update to topics
LouisLeNezet May 22, 2026
42425dd
Update to topics
LouisLeNezet May 22, 2026
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32 changes: 3 additions & 29 deletions modules/nf-core/hostile/clean/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ process HOSTILE_CLEAN {
output:
tuple val(meta), path('*.fastq.gz'), emit: fastq
tuple val(meta), path('*.json') , emit: json
path 'versions.yml' , emit: versions
tuple val("${task.process}"), val('hostile'), eval("hostile --version"), emit: versions_hostile, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -39,42 +39,16 @@ process HOSTILE_CLEAN {
--reorder \\
--airplane \\
| tee > ${prefix}.json

cat <<-END_VERSIONS > versions.yml
"${task.process}":
hostile: \$(hostile --version)
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def sorted_reads = meta.single_end ? [reads].flatten() : reads.sort { read -> read.simpleName }
def reads_cmd = meta.single_end ? "--fastq1 ${sorted_reads[0]}" : "--fastq1 ${sorted_reads[0]} --fastq2 ${sorted_reads[1]}"
def fake_read2 = !meta.single_end ? "echo '' | gzip -c > ${prefix}.clean_2.fastq.gz" : ""
def fake_read2 = !meta.single_end ? "echo '' | gzip > ${prefix}.clean_2.fastq.gz" : ""
"""
export HOSTILE_CACHE_DIR=${reference_dir}

echo "hostile \\
clean \\
${args} \\
--threads ${task.cpus} \\
${reads_cmd} \\
--index ${reference_name} \\
--output . \\
--reorder \\
--airplane \\
| tee > ${prefix}.json"

export HOSTILE_CACHE_DIR=${reference_dir}
echo "" | gzip -c > ${prefix}.clean_1.fastq.gz
echo "" | gzip > ${prefix}.clean_1.fastq.gz
${fake_read2}

touch ${prefix}.json

cat <<-END_VERSIONS > versions.yml
"${task.process}":
hostile: \$(hostile --version)
END_VERSIONS
"""
}
32 changes: 22 additions & 10 deletions modules/nf-core/hostile/clean/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "hostile_clean"
description: Removes host reads from short- and long-read FASTQ sequencing files
keywords:
Expand All @@ -14,9 +13,9 @@ tools:
documentation: "https://github.com/bede/hostile"
tool_dev_url: "https://github.com/bede/hostile"
doi: "10.1093/bioinformatics/btad728"
licence: ["MIT"]
licence:
- "MIT"
identifier: biotools:hostile

input:
- - meta:
type: map
Expand All @@ -41,7 +40,6 @@ input:
indices AND explicitly specify `--aligner bowtie2`
ontologies:
- edam: "http://edamontology.org/data_1049"

output:
fastq:
- - meta:
Expand Down Expand Up @@ -69,13 +67,27 @@ output:
pattern: "*.json"
ontologies:
- edam: "http://edamontology.org/format_3464"
versions_hostile:
- - ${task.process}:
type: string
description: The name of the process
- hostile:
type: string
description: The name of the tool
- hostile --version:
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
- hostile:
type: string
description: The name of the tool
- hostile --version:
type: eval
description: The expression to obtain the version of the tool
authors:
- "@jfy133"
maintainers:
Expand Down
19 changes: 5 additions & 14 deletions modules/nf-core/hostile/clean/tests/main.nf.test
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Expand Up @@ -46,12 +46,8 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.fastq,
process.out.versions,
path(process.out.versions.get(0)).yaml,
path(process.out.json[0][1]).readLines().any{ it.contains('\"reads_removed\": 0')}
).match() }
{ assert path(process.out.json[0][1]).readLines().any{ it.contains('\"reads_removed\": 0')} },
{ assert snapshot(sanitizeOutput(process.out, unstableKeys:["json"])).match() }
)
}

Expand Down Expand Up @@ -80,12 +76,8 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.fastq,
process.out.versions,
path(process.out.versions.get(0)).yaml,
path(process.out.json[0][1]).readLines().any{ it.contains('\"reads_removed\": 0')}
).match() }
{ assert path(process.out.json[0][1]).readLines().any{ it.contains('\"reads_removed\": 0')} },
{ assert snapshot(sanitizeOutput(process.out, unstableKeys:["json"])).match() }
)
}

Expand Down Expand Up @@ -113,8 +105,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert path(process.out.versions.get(0)).yaml}
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand Down
131 changes: 66 additions & 65 deletions modules/nf-core/hostile/clean/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"fastq - single-end - stub": {
"content": [
{
"0": [
"fastq": [
[
{
"id": "test",
Expand All @@ -11,7 +11,7 @@
"test.clean_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [
"json": [
[
{
"id": "test",
Expand All @@ -20,93 +20,94 @@
"test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
"versions.yml:md5,ada5e72cc34942b0eccc41d073c4247f"
],
"versions_hostile": [
[
"HOSTILE_CLEAN",
"hostile",
"2.0.2"
]
]
}
],
"timestamp": "2026-05-22T10:10:32.316335997",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"fastq - paired-end": {
"content": [
{
"fastq": [
[
{
"id": "test",
"single_end": true
"single_end": false
},
"test.clean_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
[
"test_1.clean_1.fastq.gz:md5,6de988b85909e6529bad0022703bcab2",
"test_2.clean_2.fastq.gz:md5,539acd65e93bf16a5ace7d6034e704c7"
]
]
],
"json": [
[
{
"id": "test",
"single_end": true
"single_end": false
},
"test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.json"
]
],
"versions": [
"versions.yml:md5,ada5e72cc34942b0eccc41d073c4247f"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
},
"timestamp": "2025-09-11T19:36:13.16472899"
},
"fastq - paired-end": {
"content": [
[
[
{
"id": "test",
"single_end": false
},
"versions_hostile": [
[
"test_1.clean_1.fastq.gz:md5,6de988b85909e6529bad0022703bcab2",
"test_2.clean_2.fastq.gz:md5,539acd65e93bf16a5ace7d6034e704c7"
"HOSTILE_CLEAN",
"hostile",
"2.0.2"
]
]
],
[
"versions.yml:md5,ada5e72cc34942b0eccc41d073c4247f"
],
{
"HOSTILE_CLEAN": {
"hostile": "2.0.2"
}
},
true
}
],
"timestamp": "2026-05-22T10:13:45.740888243",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-11-09T16:15:42.374481236"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"fastq - single-end": {
"content": [
[
[
{
"id": "test",
"single_end": true
},
"test_1.clean.fastq.gz:md5,9224ada21765cb3ad5fc05f40df78f17"
]
],
[
"versions.yml:md5,ada5e72cc34942b0eccc41d073c4247f"
],
{
"HOSTILE_CLEAN": {
"hostile": "2.0.2"
}
},
true
"fastq": [
[
{
"id": "test",
"single_end": true
},
"test_1.clean.fastq.gz:md5,9224ada21765cb3ad5fc05f40df78f17"
]
],
"json": [
[
{
"id": "test",
"single_end": true
},
"test.json"
]
],
"versions_hostile": [
[
"HOSTILE_CLEAN",
"hostile",
"2.0.2"
]
]
}
],
"timestamp": "2026-05-22T10:13:22.374303854",
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-11T09:45:14.395763629"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
}
}
13 changes: 1 addition & 12 deletions modules/nf-core/hostile/fetch/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ process HOSTILE_FETCH {

output:
tuple val(index_name), path('reference/'), emit: reference
path 'versions.yml', emit: versions
tuple val("${task.process}"), val('hostile'), eval("hostile --version"), emit: versions_hostile, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -27,29 +27,18 @@ process HOSTILE_FETCH {
fetch \\
--name ${index_name} \\
${args}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
hostile: \$(hostile --version)
END_VERSIONS
"""

stub:
"""
mkdir reference/
export HOSTILE_CACHE_DIR=./reference

touch reference/human-t2t-hla.1.bt2
touch reference/human-t2t-hla.2.bt2
touch reference/human-t2t-hla.3.bt2
touch reference/human-t2t-hla.4.bt2
touch reference/human-t2t-hla.rev.1.bt2
touch reference/human-t2t-hla.rev.2.bt2
touch reference/human-t2t-hla.mmi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
hostile: \$(hostile --version)
END_VERSIONS
"""
}
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