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Concoct/concoctcoveragetable modules updates #5868

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merged 5 commits into from
Jun 21, 2024
Merged

Concoct/concoctcoveragetable modules updates #5868

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09d530e
Bump concoct/cutupfasta version, add stub, add nf-test
jfy133 Jun 21, 2024
ac6542a
Bump conda build, add stub and nf-test for CONCOT/concoctcoveragetable
jfy133 Jun 21, 2024
a7a2f5c
Merge branch 'master' into concoct-modules-updates
jfy133 Jun 21, 2024
eec3616
Merge branch 'master' into concoct-modules-updates
jfy133 Jun 21, 2024
5cb0b4a
Remove pytest entry
aidaanva Jun 21, 2024
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16 changes: 14 additions & 2 deletions modules/nf-core/concoct/concoctcoveragetable/main.nf
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Expand Up @@ -5,8 +5,8 @@ process CONCOCT_CONCOCTCOVERAGETABLE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py311h245ed52_4':
'biocontainers/concoct:1.1.0--py311h245ed52_4' }"
'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py312h245ed52_6':
'biocontainers/concoct:1.1.0--py312h245ed52_6' }"

input:
tuple val(meta), path(bed), path(bamfiles), path(baifiles)
Expand All @@ -33,4 +33,16 @@ process CONCOCT_CONCOCTCOVERAGETABLE {
concoct: \$(echo \$(concoct --version 2>&1) | sed 's/concoct //g' )
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
concoct: \$(echo \$(concoct --version 2>&1) | sed 's/concoct //g' )
END_VERSIONS
"""
}
2 changes: 1 addition & 1 deletion modules/nf-core/concoct/concoctcoveragetable/meta.yml
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Expand Up @@ -16,7 +16,7 @@ tools:
documentation: "https://concoct.readthedocs.io/en/latest/index.html"
tool_dev_url: "https://github.com/BinPro/CONCOCT"
doi: "10.1038/nmeth.3103"
licence: "['FreeBSD']"
licence: ["FreeBSD"]
input:
- meta:
type: map
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99 changes: 99 additions & 0 deletions modules/nf-core/concoct/concoctcoveragetable/tests/main.nf.test
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@@ -0,0 +1,99 @@
nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "concoct"
tag "concoct/concoctcoveragetable"
tag "concoct/cutupfasta"

setup {
run("CONCOCT_CUTUPFASTA") {
script "../../cutupfasta/main.nf"
process {
"""
input[0] = [
[id: 'test', single_end: false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = true
"""
}
}
}

test("sarscov2 - bam") {

when {
process {
"""
ch_bam_input = Channel
.fromList([
[
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
],
[
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
]
]
])


input[0] = CONCOCT_CUTUPFASTA.out.bed.join( ch_bam_input )
"""
}
}

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

}

test("sarscov2 - bam - stub") {

options "-stub"

when {
process {
"""
ch_bam_input = Channel
.fromList([
[
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
],
[
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
]
]
])

input[0] = CONCOCT_CUTUPFASTA.out.bed.join( ch_bam_input )
"""
}
}

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

}

}
60 changes: 60 additions & 0 deletions modules/nf-core/concoct/concoctcoveragetable/tests/main.nf.test.snap
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@@ -0,0 +1,60 @@
{
"sarscov2 - bam - stub": {
"content": [
{
"0": [

],
"1": [

],
"tsv": [

],
"versions": [

]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-21T16:02:03.884676509"
},
"sarscov2 - bam": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.tsv:md5,0183c95ec03d2a6c83a4ca82935308a4"
]
],
"1": [
"versions.yml:md5,156a9a23e05b34188d03d52b39fae343"
],
"tsv": [
[
{
"id": "test",
"single_end": false
},
"test.tsv:md5,0183c95ec03d2a6c83a4ca82935308a4"
]
],
"versions": [
"versions.yml:md5,156a9a23e05b34188d03d52b39fae343"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-21T15:59:09.328659542"
}
}
2 changes: 2 additions & 0 deletions modules/nf-core/concoct/concoctcoveragetable/tests/tags.yml
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@@ -0,0 +1,2 @@
concoct/concoctcoveragetable:
- "modules/nf-core/concoct/concoctcoveragetable/**"
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Expand Up @@ -284,9 +284,6 @@ cnvnator/convert2vcf:
concoct/concoct:
- modules/nf-core/concoct/concoct/**
- tests/modules/nf-core/concoct/concoct/**
concoct/concoctcoveragetable:
- modules/nf-core/concoct/concoctcoveragetable/**
- tests/modules/nf-core/concoct/concoctcoveragetable/**
concoct/extractfastabins:
- modules/nf-core/concoct/extractfastabins/**
- tests/modules/nf-core/concoct/extractfastabins/**
Expand Down
35 changes: 0 additions & 35 deletions tests/modules/nf-core/concoct/concoctcoveragetable/main.nf
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5 changes: 0 additions & 5 deletions tests/modules/nf-core/concoct/concoctcoveragetable/nextflow.config
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8 changes: 0 additions & 8 deletions tests/modules/nf-core/concoct/concoctcoveragetable/test.yml
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