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new module pangolin/updatedata & patch pangolin/run #7182

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merged 8 commits into from
Dec 10, 2024
Merged

new module pangolin/updatedata & patch pangolin/run #7182

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4eb5f73
new module pangolin-updatedataset
Joon-Klaps Dec 9, 2024
370c0dc
update pangolin/run & snapshots
Joon-Klaps Dec 9, 2024
2ab1ce0
update meta.yml plus snapshots
Joon-Klaps Dec 10, 2024
0217718
Merge branch 'master' into pangolin-updatedb
Joon-Klaps Dec 10, 2024
12b8681
fix nf-core linting
Joon-Klaps Dec 10, 2024
45e19ad
Merge branch 'pangolin-updatedb' of https://github.com/nf-core/module…
Joon-Klaps Dec 10, 2024
6842ff9
update test to check for header
Joon-Klaps Dec 10, 2024
b9e50d6
Merge branch 'master' into pangolin-updatedb
Joon-Klaps Dec 10, 2024
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0 modules/nf-core/pangolin/environment.yml → modules/nf-core/pangolin/run/environment.yml
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18 changes: 17 additions & 1 deletion modules/nf-core/pangolin/main.nf → modules/nf-core/pangolin/run/main.nf
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
process PANGOLIN {
process PANGOLIN_RUN {
tag "$meta.id"
label 'process_medium'

Expand All @@ -9,6 +9,7 @@ process PANGOLIN {

input:
tuple val(meta), path(fasta)
path(db)

output:
tuple val(meta), path('*.csv'), emit: report
Expand All @@ -20,11 +21,13 @@ process PANGOLIN {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def db_command = db ? "--datadir ${db}" : ''
"""
export XDG_CACHE_HOME=/tmp/.cache

pangolin \\
$fasta\\
$db_command \\
--outfile ${prefix}.pangolin.csv \\
--threads $task.cpus \\
$args
Expand All @@ -34,4 +37,17 @@ process PANGOLIN {
pangolin: \$(pangolin --version | sed "s/pangolin //g")
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
export XDG_CACHE_HOME=/tmp/.cache

touch ${prefix}.pangolin.csv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pangolin: \$(pangolin --version | sed "s/pangolin //g")
END_VERSIONS
"""
}
8 changes: 7 additions & 1 deletion modules/nf-core/pangolin/meta.yml → modules/nf-core/pangolin/run/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
name: pangolin
name: pangolin_run
description: Phylogenetic Assignment of Named Global Outbreak LINeages
keywords:
- covid
- pangolin
- lineage
- run
tools:
- pangolin:
description: |
Expand All @@ -21,6 +22,11 @@ input:
type: file
description: |
The genome assembly to be evaluated
- - db:
type: directory
description: |
Directory containing the Pangolin database

output:
- report:
- meta:
Expand Down
99 changes: 99 additions & 0 deletions modules/nf-core/pangolin/run/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -0,0 +1,99 @@
nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "pangolin/updatedata"
tag "pangolin/run"
tag "pangolin"

test("sarscov2 genome [fasta]") {

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
]
input[1] = []
"""
}
}

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

}

test("sarscov2 genome [fasta] - update data") {
setup{
run("PANGOLIN_UPDATEDATA") {
script "../../updatedata/main.nf"
process {
"""
input[0] = 'testdb'
"""
}
}
}

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
]
input[1] = PANGOLIN_UPDATEDATA.out.db
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert path(process.out.report[0][1]).readLines().first().contains("taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note") },
{ assert snapshot(
file(process.out.report[0][1]).name,
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process.out.versions
).match()
}
)
}
}

test("sarscov2 genome [fasta] - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
]
input[1] = []
"""
}
}

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

}


}
37 changes: 25 additions & 12 deletions .../nf-core/pangolin/tests/main.nf.test.snap → ...core/pangolin/run/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -7,30 +7,43 @@
{
"id": "test"
},
"test.pangolin.csv:md5,2cc701567cf37bad5c6574c29aa595d4"
"test.pangolin.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,65ec45a19faa92a922073b9b08d90a8a"
"versions.yml:md5,4e70f8b44182b5be5eb0b706c2c551bd"
],
"report": [
[
{
"id": "test"
},
"test.pangolin.csv:md5,2cc701567cf37bad5c6574c29aa595d4"
"test.pangolin.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,65ec45a19faa92a922073b9b08d90a8a"
"versions.yml:md5,4e70f8b44182b5be5eb0b706c2c551bd"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-09T16:27:30.099020683"
},
"sarscov2 genome [fasta] - update data": {
"content": [
"test.pangolin.csv",
[
"versions.yml:md5,4e70f8b44182b5be5eb0b706c2c551bd"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-10-18T10:33:48.797026222"
"timestamp": "2024-12-09T16:36:50.212759186"
},
"sarscov2 genome [fasta]": {
"content": [
Expand All @@ -44,7 +57,7 @@
]
],
"1": [
"versions.yml:md5,65ec45a19faa92a922073b9b08d90a8a"
"versions.yml:md5,4e70f8b44182b5be5eb0b706c2c551bd"
],
"report": [
[
Expand All @@ -55,14 +68,14 @@
]
],
"versions": [
"versions.yml:md5,65ec45a19faa92a922073b9b08d90a8a"
"versions.yml:md5,4e70f8b44182b5be5eb0b706c2c551bd"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-10-18T10:33:17.535254436"
"timestamp": "2024-12-09T16:25:48.834093927"
}
}
57 changes: 0 additions & 57 deletions modules/nf-core/pangolin/tests/main.nf.test
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7 changes: 7 additions & 0 deletions modules/nf-core/pangolin/updatedata/environment.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
channels:
- conda-forge
- bioconda
dependencies:
- bioconda::pangolin-data=1.30
- bioconda::pangolin=4.3
- bioconda::snakemake=7.30.1
49 changes: 49 additions & 0 deletions modules/nf-core/pangolin/updatedata/main.nf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,49 @@
process PANGOLIN_UPDATEDATA {
tag "$dbname"
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bb/bb7bac48e43a9cd6274e1f99c761a5785b74f6d8a55313ee634aaffbe87c1869/data' :
'community.wave.seqera.io/library/pangolin-data_pangolin_snakemake:5bbc297f7502ff33' }"

input:
val(dbname)

output:
path("${prefix}") , emit: db
path "versions.yml" , emit: versions

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

script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${dbname}"
"""
export XDG_CACHE_HOME=/tmp/.cache
mkdir -p ${prefix}

pangolin \\
$args \\
--update-data \\
--threads $task.cpus \\
--datadir ${prefix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pangolin: \$(pangolin --version | sed "s/pangolin //g")
END_VERSIONS
"""

stub:
prefix = task.ext.prefix ?: "${dbname}"
"""
mkdir -p ${prefix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pangolin: \$(pangolin --version | sed "s/pangolin //g")
END_VERSIONS
"""
}
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