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port tiddit-sv to nf-test and add --threads #5371

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merged 9 commits into from
Mar 22, 2024
Merged

port tiddit-sv to nf-test and add --threads #5371

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8a15aa9
start porting
famosab Mar 22, 2024
6e7e1b7
fix con
famosab Mar 22, 2024
031ff6f
adjust tests and add snapshot
famosab Mar 22, 2024
65417f4
add threads argument
famosab Mar 22, 2024
c770395
remove old pytest files
famosab Mar 22, 2024
e58ef1d
add bwa/index tag
famosab Mar 22, 2024
ddc9bea
fix meta for linting
famosab Mar 22, 2024
afd19cc
update assertions to include more
famosab Mar 22, 2024
e91f63a
modify meta map
famosab Mar 22, 2024
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1 change: 1 addition & 0 deletions modules/nf-core/tiddit/sv/main.nf
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Expand Up @@ -31,6 +31,7 @@ process TIDDIT_SV {
tiddit \\
--sv \\
$args \\
--threads $task.cpus \\
--bam $input \\
--ref $fasta \\
-o $prefix
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12 changes: 11 additions & 1 deletion modules/nf-core/tiddit/sv/meta.yml
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Expand Up @@ -21,14 +21,24 @@ input:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram}"
- index:
- input_index:
type: file
description: BAM/CRAM index file
pattern: "*.{bai,crai}"
- meta2:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'test_fasta']`
- fasta:
type: file
description: Input FASTA file
pattern: "*.{fasta,fa}"
- meta3:
type: map
description: |
Groovy Map containing sample information from bwa index
e.g. `[ id:'test_bwa-index' ]`
- bwa_index:
type: file
description: BWA genome index files
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193 changes: 193 additions & 0 deletions modules/nf-core/tiddit/sv/tests/main.nf.test
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@@ -0,0 +1,193 @@
nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "tiddit"
tag "tiddit/sv"
tag "bwa/index"

test("sarscov2 - bam - bwa") {

setup {

run("BWA_INDEX") {
script "../../../../nf-core/bwa/index/main.nf"
process {
"""
input[0] = [ [id: 'test'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
"""
}
}
}

when {
process {
"""
input[0] = [ [ id:'test' ], // meta map
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.paired_end.sorted.bam.bai', checkIfExists: true)
]
// fasta
input[1] = [ [id: 'test'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
// bwa_index
input[2] = BWA_INDEX.out.index
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.1") },
{ assert path(process.out.ploidy.get(0).get(1)).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") },
{ assert snapshot(process.out.versions).match("bam_bwa_version") }
)
}

}

test("sarscov2 - bam - no_bwa") {

config "./nextflow.config"

when {
process {
"""
input[0] = [ [ id:'test' ], // meta map
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.paired_end.sorted.bam.bai', checkIfExists: true)
]
// fasta
input[1] = [ [id: 'test'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
// bwa_index
input[2] = [ [], [] ]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.1") },
{ assert path(process.out.ploidy.get(0).get(1)).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") },
{ assert snapshot(process.out.versions).match("bam_version") }
)
}

}

test("human - cram - bwa") {

setup {

run("BWA_INDEX") {
script "../../../../nf-core/bwa/index/main.nf"
process {
"""
input[0] = [ [id: 'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
]
"""
}
}
}

when {
process {
"""
input[0] = [ [ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
]
// fasta
input[1] = [ [id: 'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
]
// bwa_index
input[2] = BWA_INDEX.out.index
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.1") },
{ assert path(process.out.ploidy.get(0).get(1)).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") },
{ assert snapshot(process.out.versions).match("cram_bwa_version") })
}

}

test("human - cram - no_bwa") {

config "./nextflow.config"

when {
process {
"""
input[0] = [ [ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
]
// fasta
input[1] = [ [id: 'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
]
// bwa_index
input[2] = [ [], [] ]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.1") },
{ assert path(process.out.ploidy.get(0).get(1)).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") },
{ assert snapshot(process.out.versions).match("cram_version") })
}

}

test("sarscov2 - bam - stub") {

options "-stub"

when {
process {
"""
input[0] = [ [ id:'test' ], // meta map
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.paired_end.sorted.bam.bai', checkIfExists: true)
]
// fasta
input[1] = [ [id: 'test'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
// bwa_index
input[2] = [ [], [] ]
"""
}
}

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

}

}
99 changes: 99 additions & 0 deletions modules/nf-core/tiddit/sv/tests/main.nf.test.snap
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5 changes: 5 additions & 0 deletions modules/nf-core/tiddit/sv/tests/nextflow.config
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@@ -0,0 +1,5 @@
process {
withName: 'TIDDIT_SV' {
ext.args = '--skip_assembly'
}
}
2 changes: 2 additions & 0 deletions modules/nf-core/tiddit/sv/tests/tags.yml
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@@ -0,0 +1,2 @@
tiddit/sv:
- "modules/nf-core/tiddit/sv/**"
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Expand Up @@ -2192,9 +2192,6 @@ tbprofiler/profile:
tiara/tiara:
- modules/nf-core/tiara/tiara/**
- tests/modules/nf-core/tiara/tiara/**
tiddit/sv:
- modules/nf-core/tiddit/sv/**
- tests/modules/nf-core/tiddit/sv/**
topas/gencons:
- modules/nf-core/topas/gencons/**
- tests/modules/nf-core/topas/gencons/**
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