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Merged
mahesh-panchal merged 1 commit into from
Apr 8, 2025
Merged

Add sylphtax/merge and update taxprof to version 1.2 #8228

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7 changes: 7 additions & 0 deletions modules/nf-core/sylphtax/merge/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::sylph-tax=1.2.0"
51 changes: 51 additions & 0 deletions modules/nf-core/sylphtax/merge/main.nf
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process SYLPHTAX_MERGE {
tag "$meta.id"
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/sylph-tax:1.2.0--pyhdfd78af_0':
'biocontainers/sylph-tax:1.2.0--pyhdfd78af_0' }"


input:
tuple val(meta), path(sylphtax_reports)
val data_type

output:
tuple val(meta), path("*.tsv"), emit: tsv
path "versions.yml" , emit: versions

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

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
export SYLPH_TAXONOMY_CONFIG="/tmp/config.json"
sylph-tax \\
merge \\
${sylphtax_reports} \\
--column $data_type \\
--output ${prefix}.tsv

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

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
export SYLPH_TAXONOMY_CONFIG="/tmp/config.json"
touch ${prefix}.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
sylph-tax: \$(sylph-tax --version)
END_VERSIONS
"""
}
46 changes: 46 additions & 0 deletions modules/nf-core/sylphtax/merge/meta.yml
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name: "sylphtax_merge"
description: Merge multiple taxonomic profiles from sylphtaxt/taxprof into a tsv table
keywords:
- sylph
- metagenomics
- merge
tools:
- sylphtax:
description: Integrating taxonomic information into the sylph metagenome profiler.
homepage: https://github.com/bluenote-1577/sylph-tax?tab=readme-ov-file
documentation: https://sylph-docs.github.io/sylph-tax/
licence: ["MIT"]
identifier: ""
input:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- sylphtax_reports:
type: file
description: Output taxonomic profile from sylph-tax taxprof command.
pattern: "*.{sylphmpa}"
- - data_type:
type: string
description: Can be ANI, relative abundance, or sequence abundance.
output:
- tsv:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- "*.tsv":
type: file
description: Output profile with the merged taxonomic profiles in tsv format.
pattern: "*.tsv"
- versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@sofstam"
maintainers:
- "@sofstam"
116 changes: 116 additions & 0 deletions modules/nf-core/sylphtax/merge/tests/main.nf.test
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nextflow_process {

name "Test Process SYLPHTAX_MERGE"
script "../main.nf"
process "SYLPHTAX_MERGE"

tag "modules"
tag "modules_nfcore"
tag "sylph"
tag "sylph/profile"
tag "sylphtax"
tag "sylphtax/taxprof"
tag "sylphtax/merge"


test("sarscov2 illumina single-end [fastq_gz]") {
setup {
run("SYLPH_PROFILE") {
script "../../../sylph/profile/main.nf"
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
]
input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
"""
}
}
run("SYLPHTAX_TAXPROF")
{
script "../../../sylphtax/taxprof/main.nf"
process {
"""
input[0] = SYLPH_PROFILE.out.profile_out
input[1] = file('https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/sylph/test_taxonomy.tsv.gz', checkIfExists: true)
"""
}
}

}
when {

process {
"""
input[0] = SYLPHTAX_TAXPROF.out.taxprof_output
input[1] = "relative_abundance"
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
process.out.tsv
).match() }
)
}

}

test("sarscov2 illumina single-end [fastq_gz]-stub") {

options '-stub'

setup {
run("SYLPH_PROFILE") {
script "../../../sylph/profile/main.nf"
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
]
input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
"""
}
}
run("SYLPHTAX_TAXPROF")
{
script "../../../sylphtax/taxprof/main.nf"
process {
"""
input[0] = SYLPH_PROFILE.out.profile_out
input[1] = file('https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/sylph/test_taxonomy.tsv.gz', checkIfExists: true)
"""
}
}

}
when {

process {
"""
input[0] = SYLPHTAX_TAXPROF.out.taxprof_output
input[1] = "relative_abundance"
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
process.out.tsv
).match() }
)
}

}
}
44 changes: 44 additions & 0 deletions modules/nf-core/sylphtax/merge/tests/main.nf.test.snap
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{
"sarscov2 illumina single-end [fastq_gz]": {
"content": [
[
"versions.yml:md5,fb665700c08de369d03e29c02394da07"
],
[
[
{
"id": "test",
"single_end": false
},
"test.tsv:md5,0babfd085a52f127c5d352fab5595b39"
]
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-07T15:29:34.708536546"
},
"sarscov2 illumina single-end [fastq_gz]-stub": {
"content": [
[
"versions.yml:md5,fb665700c08de369d03e29c02394da07"
],
[
[
{
"id": "test",
"single_end": false
},
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-07T15:29:46.390759044"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/sylphtax/taxprof/environment.yml
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Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::sylph-tax=1.1.2"
- "bioconda::sylph-tax=1.2.0"
12 changes: 7 additions & 5 deletions modules/nf-core/sylphtax/taxprof/main.nf
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Expand Up @@ -5,8 +5,8 @@ process SYLPHTAX_TAXPROF {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/sylph-tax:1.1.2--pyhdfd78af_0':
'biocontainers/sylph-tax:1.1.2--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/sylph-tax:1.2.0--pyhdfd78af_0':
'biocontainers/sylph-tax:1.2.0--pyhdfd78af_0' }"

input:
tuple val(meta), path(sylph_results)
Expand All @@ -24,28 +24,30 @@ process SYLPHTAX_TAXPROF {
def prefix = task.ext.prefix ?: "${meta.id}"

"""
export SYLPH_TAXONOMY_CONFIG="/tmp/config.json"
sylph-tax \\
taxprof \\
$sylph_results \\
$args \\
-t $taxonomy

mv *.sylphmpa ${prefix}.sylphmpa

cat <<-END_VERSIONS > versions.yml
"${task.process}":
sylph-tax: \$(sylph-tax --version 2>&1 | sed -n 's/.*\\([0-9]\\+\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p' | head -n 1)
sylph-tax: \$(sylph-tax --version)
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
export SYLPH_TAXONOMY_CONFIG="/tmp/config.json"
touch ${prefix}.sylphmpa

cat <<-END_VERSIONS > versions.yml
"${task.process}":
sylph-tax: \$(sylph-tax --version 2>&1 | sed -n 's/.*\\([0-9]\\+\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p' | head -n 1)
sylph-tax: \$(sylph-tax --version)
END_VERSIONS
"""
}
10 changes: 5 additions & 5 deletions modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap
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Expand Up @@ -2,7 +2,7 @@
"stub sarscov2 illumina single-end [fastq_gz]": {
"content": [
[
"versions.yml:md5,976fae8d146f4f3087e2a090703f09b9"
"versions.yml:md5,bdbbd22b3e721ba2027d3e6cb1dc4bb4"
],
[
[
Expand All @@ -17,27 +17,27 @@
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-06T09:50:24.907781877"
"timestamp": "2025-04-07T15:28:04.026470884"
},
"sarscov2 illumina single-end [fastq_gz]": {
"content": [
[
"versions.yml:md5,976fae8d146f4f3087e2a090703f09b9"
"versions.yml:md5,bdbbd22b3e721ba2027d3e6cb1dc4bb4"
],
[
[
{
"id": "test",
"single_end": true
},
"test.sylphmpa:md5,797e3463eeb9a2e8f91de9b842cd421d"
"test.sylphmpa:md5,a9743c21a53ba766226e57d2a25f6167"
]
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-03-06T09:50:17.295239617"
"timestamp": "2025-04-07T15:27:55.45776116"
}
}
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