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Swap ngscheckmate/ncm to nftest #5679

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merged 2 commits into from
May 23, 2024
Merged

Swap ngscheckmate/ncm to nftest #5679

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35ffc8d
Swap ngscheckmate/ncm to nftest
SPPearce May 23, 2024
fc40975
Update main.nf.test
SPPearce May 23, 2024
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1 change: 1 addition & 0 deletions modules/nf-core/ngscheckmate/ncm/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,7 @@ process NGSCHECKMATE_NCM {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "$meta.id"
"""
touch ${prefix}_output_corr_matrix.txt
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5 changes: 5 additions & 0 deletions modules/nf-core/ngscheckmate/ncm/tests/bam.config
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@@ -0,0 +1,5 @@
process {
withName: NGSCHECKMATE_NCM {
ext.args = '-B'
}
}
184 changes: 184 additions & 0 deletions modules/nf-core/ngscheckmate/ncm/tests/main.nf.test
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@@ -0,0 +1,184 @@
nextflow_process {

name "Test Process NGSCHECKMATE_NCM"
script "../main.nf"
process "NGSCHECKMATE_NCM"
config "./nextflow.config"

tag "modules"
tag "modules_nfcore"
tag "ngscheckmate"
tag "ngscheckmate/ncm"
tag "bedtools/makewindows"
tag "bcftools/mpileup"

setup {

run("BEDTOOLS_MAKEWINDOWS") {
script "../../../bedtools/makewindows/main.nf"
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@SPPearce @nvnieuwk : Will that work in a pipeline where bedtools isn't installed? I'm having problems running this nf-test in Sarek where we don't have bedtools installed. The nf-test ran better after I installed bedtools in Sarek, but that doesn't seem like the right solution to me 🤔

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That's a good point! Maybe this is something that can be handled by nf-core tools (@mirpedrol)

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Hmmm.
The alternative would be to add files to test_data instead, but there are quite a few modules that do this kind of setup block. This is essentially taking a bed file and splitting it into individual bases.
I guess BCFTOOLS_MPILEUP exists in sarek already, so you didn't have an issue with that part.

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@asp8200 asp8200 Jun 6, 2024 •
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BCFTOOLS_MPILEUP is installed in Sarek, so that didn't cause any issues. However, I guess the nf-test should be kind of self-contained, and not rely on what other modules might or might not be installed in the particular pipeline that is trying to use the module.

I also had to change all params.test_data... to params.modules_testdata_base_path... to get the test kind of work, that is, I managed to get 3 out of 4 "subtests" working:

maxulysse/nf-core_sarek#7

process {
"""
input[0] = [ [ id:'test' ],
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
]
"""
}
}

run("BCFTOOLS_MPILEUP", alias: "BCFTOOLS_MPILEUP1") {
script "../../../bcftools/mpileup/main.nf"
process {
"""
input[0] = [
[ id:'test1' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
]
input[1] = [ [ id:'sarscov2' ],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
input[2] = false
"""
}
}

run("BCFTOOLS_MPILEUP", alias: "BCFTOOLS_MPILEUP2") {
script "../../../bcftools/mpileup/main.nf"
process {
"""
input[0] = [
[ id:'test2' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
]
input[1] = [ [ id:'sarscov2' ],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
input[2] = false
"""
}
}

}


test("sarscov2 - bam") {
config "./bam.config"
when {
process {
"""
input[0] = [ [ id: 'combined_bams' ],
[file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'] , checkIfExists: true ),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'] , checkIfExists: true ),
file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'] , checkIfExists: true ),
file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true )
]
]
input[1] = BEDTOOLS_MAKEWINDOWS.out.bed
input[2] = [ [ id:'sarscov2' ],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.corr_matrix,
process.out.matched,
process.out.all,
process.out.versions
).match() }
)
}

}

test("sarscov2 - vcf") {
config "./vcf.config"
when {
process {
"""
input[0] = BCFTOOLS_MPILEUP1.out.vcf.combine(BCFTOOLS_MPILEUP2.out.vcf.map{it[1]}).map{meta, one, two -> [meta, [one, two]]}.map{meta, stuff -> [meta, stuff.flatten()]}
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This is horrific and could do with cleaning up...
I have two outputs that are both:
[meta, vcf]
and I want to make
[new_meta, [vcf1, vcf2]]

input[1] = BEDTOOLS_MAKEWINDOWS.out.bed
input[2] = [ [ id:'sarscov2' ],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.corr_matrix,
process.out.matched,
process.out.all,
file(process.out.pdf[0][1]).name,
process.out.versions
).match() }
)
}

}

test("sarscov2 - bam - stub") {

options "-stub"
config "./bam.config"
when {
process {
"""
input[0] = [ [ id: 'combined_bams' ],
[file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'] , checkIfExists: true ),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'] , checkIfExists: true ),
file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'] , checkIfExists: true ),
file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true )
]
]
input[1] = BEDTOOLS_MAKEWINDOWS.out.bed
input[2] = [ [ id:'sarscov2' ],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
"""
}
}

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

}

test("sarscov2 - vcf - stub") {

options "-stub"
config "./vcf.config"
when {
process {
"""
input[0] = BCFTOOLS_MPILEUP1.out.vcf.combine(BCFTOOLS_MPILEUP2.out.vcf.map{it[1]})
input[1] = BEDTOOLS_MAKEWINDOWS.out.bed
input[2] = [ [ id:'sarscov2' ],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
"""
}
}

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

}

}
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