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Issue 348 #419

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merged 5 commits into from
Oct 11, 2024
Merged

Issue 348 #419

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97da60f
Added BED to SV calling
Schmytzi Oct 8, 2024
ac48551
Add comment to ch_bed
Schmytzi Oct 8, 2024
8bb6f50
Updated Changelog
Schmytzi Oct 8, 2024
05dcd39
Updated tests
Schmytzi Oct 8, 2024
321462f
Updated BED in tests to capture variants
Schmytzi Oct 11, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#393](https://github.com/genomic-medicine-sweden/nallo/pull/393) - Added a new `--minimap2_read_mapping_preset` parameter
- [#403](https://github.com/genomic-medicine-sweden/nallo/pull/403) - Added `FOUND_IN=hificnv` tags to CNV calling output
- [#417](https://github.com/genomic-medicine-sweden/nallo/pull/417) - Added `FOUND_IN=deepvariant` tags to SNV calling output
- [#419](https://github.com/genomic-medicine-sweden/nallo/pull/419) - Added support for SV filtering using input BED file ([#348](https://github.com/genomic-medicine-sweden/nallo/issues/348))

### `Changed`

Expand Down
3 changes: 2 additions & 1 deletion subworkflows/local/call_svs/main.nf
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Expand Up @@ -14,6 +14,7 @@ workflow CALL_SVS {
ch_fai // channel [mandatory]: [ val(meta), path(fai) ]
sv_caller // val [mandatory]: Which caller to use
ch_tandem_repeats // channel [optional]: [ val(meta), path(bed) ]
ch_bed // channel [optional]: [ val(meta), path(bed) ]

main:
ch_versions = Channel.empty()
Expand Down Expand Up @@ -82,7 +83,7 @@ workflow CALL_SVS {
.set { ch_bcftools_merge_in }

// Merge the files with new sample names
BCFTOOLS_MERGE ( ch_bcftools_merge_in, ch_fasta, ch_fai, [[],[]] )
BCFTOOLS_MERGE ( ch_bcftools_merge_in, ch_fasta, ch_fai, ch_bed )
ch_versions = ch_versions.mix(BCFTOOLS_MERGE.out.versions)

emit:
Expand Down
172 changes: 160 additions & 12 deletions subworkflows/local/call_svs/tests/main.nf.test
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Expand Up @@ -31,7 +31,7 @@ nextflow_workflow {
}
}

test("1 sample - [bam, bai], fasta, fai, [] - sniffles") {
test("1 sample - [bam, bai], fasta, fai, [], [] - sniffles") {

when {
workflow {
Expand All @@ -45,6 +45,7 @@ nextflow_workflow {
input[2] = SAMTOOLS_FAIDX.out.fai
input[3] = "sniffles"
input[4] = [[],[]]
input[5] = [[],[]]
"""
}
}
Expand All @@ -64,7 +65,7 @@ nextflow_workflow {

}

test("1 sample - [bam, bai], fasta, fai, bed - sniffles") {
test("1 sample - [bam, bai], fasta, fai, bed, [] - sniffles") {

when {
workflow {
Expand All @@ -81,6 +82,7 @@ nextflow_workflow {
[ id:'trf' ],
file('https://github.com/fritzsedlazeck/Sniffles/raw/master/annotations/human_GRCh38_no_alt_analysis_set.trf.bed', checkIfExists: true)
]
input[5] = [[],[]]
"""
}
}
Expand All @@ -100,7 +102,7 @@ nextflow_workflow {

}

test("2 samples - [bam, bai], fasta, fai, [] - sniffles") {
test("2 samples - [bam, bai], fasta, fai, [], [] - sniffles") {

when {
workflow {
Expand All @@ -121,6 +123,7 @@ nextflow_workflow {
input[2] = SAMTOOLS_FAIDX.out.fai
input[3] = "sniffles"
input[4] = [[],[]]
input[5] = [[],[]]
"""
}
}
Expand All @@ -141,7 +144,43 @@ nextflow_workflow {

}

test("1 sample - [bam, bai], fasta, fai, [] - severus") {
test("1 sample - [bam, bai], fasta, fai, [], bed - sniffles") {

when {
workflow {
"""
input[0] = Channel.of([
[ id:'test', single_end:false, project: 'project' ], // meta map
file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
])
input[1] = GUNZIP.out.gunzip
input[2] = SAMTOOLS_FAIDX.out.fai
input[3] = "sniffles"
input[4] = [[],[]]
input[5] = Channel.of('chr20\t2650000\t2660000')
.collectFile(name: 'chr20.bed', newLine: true)
.map{ file -> [ [ id:'chr20'], file ] }
"""
}
}

then {
assertAll(
{ assert workflow.success },
{ assert workflow.out.ch_sv_calls_tbi.get(0).get(1).endsWith("tbi") },
{ assert workflow.out.ch_multisample_tbi.get(0).get(1).endsWith("tbi") },
{ assert snapshot(
path(workflow.out.ch_sv_calls_vcf.get(0).get(1)).vcf.variantsMD5,
path(workflow.out.ch_multisample_vcf.get(0).get(1)).vcf.variantsMD5,
workflow.out.versions,
).match() }
)
}

}

test("1 sample - [bam, bai], fasta, fai, [], [] - severus") {

when {
workflow {
Expand All @@ -155,6 +194,7 @@ nextflow_workflow {
input[2] = SAMTOOLS_FAIDX.out.fai
input[3] = "severus"
input[4] = [[],[]]
input[5] = [[],[]]
"""
}
}
Expand All @@ -174,7 +214,7 @@ nextflow_workflow {

}

test("1 sample - [bam, bai], fasta, fai, bed - severus") {
test("1 sample - [bam, bai], fasta, fai, bed, [] - severus") {

when {
workflow {
Expand All @@ -191,6 +231,43 @@ nextflow_workflow {
[ id:'trf' ],
file('https://github.com/fritzsedlazeck/Sniffles/raw/master/annotations/human_GRCh38_no_alt_analysis_set.trf.bed', checkIfExists: true)
]
input[5] = [[],[]]
"""
}
}

then {
assertAll(
{ assert workflow.success },
{ assert workflow.out.ch_sv_calls_tbi.get(0).get(1).endsWith("tbi") },
{ assert workflow.out.ch_multisample_tbi.get(0).get(1).endsWith("tbi") },
{ assert snapshot(
path(workflow.out.ch_sv_calls_vcf.get(0).get(1)).vcf.variantsMD5,
path(workflow.out.ch_multisample_vcf.get(0).get(1)).vcf.variantsMD5,
workflow.out.versions,
).match() }
)
}

}

test("1 sample - [bam, bai], fasta, fai, [], bed - severus") {

when {
workflow {
"""
input[0] = Channel.of([
[ id:'test', single_end:false, project: 'project' ], // meta map
file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
])
input[1] = GUNZIP.out.gunzip
input[2] = SAMTOOLS_FAIDX.out.fai
input[3] = "severus"
input[4] = [[],[]]
input[5] = Channel.of('chr20\t2650000\t2660000')
.collectFile(name: 'chr20.bed', newLine: true)
.map{ file -> [ [ id:'chr20'], file ] }
"""
}
}
Expand All @@ -210,7 +287,7 @@ nextflow_workflow {

}

test("2 samples - [bam, bai], fasta, fai, [] - severus") {
test("2 samples - [bam, bai], fasta, fai, [], [] - severus") {

when {
workflow {
Expand All @@ -231,6 +308,7 @@ nextflow_workflow {
input[2] = SAMTOOLS_FAIDX.out.fai
input[3] = "severus"
input[4] = [[],[]]
input[5] = [[],[]]
"""
}
}
Expand All @@ -251,7 +329,7 @@ nextflow_workflow {

}

test("1 sample - [bam, bai], fasta, fai, [] - sniffles -stub") {
test("1 sample - [bam, bai], fasta, fai, [], [] - sniffles -stub") {

options "-stub"

Expand All @@ -267,6 +345,7 @@ nextflow_workflow {
input[2] = SAMTOOLS_FAIDX.out.fai
input[3] = "sniffles"
input[4] = [[],[]]
input[5] = [[],[]]
"""
}
}
Expand All @@ -280,7 +359,7 @@ nextflow_workflow {

}

test("1 sample - [bam, bai], fasta, fai, bed - sniffles -stub") {
test("1 sample - [bam, bai], fasta, fai, bed, [] - sniffles -stub") {

options "-stub"

Expand All @@ -299,6 +378,39 @@ nextflow_workflow {
[ id:'trf' ],
file('https://github.com/fritzsedlazeck/Sniffles/raw/master/annotations/human_GRCh38_no_alt_analysis_set.trf.bed', checkIfExists: true)
]
input[5] = [[],[]]
"""
}
}

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

}

test("1 sample - [bam, bai], fasta, fai, [], bed - sniffles -stub") {

options "-stub"

when {
workflow {
"""
input[0] = Channel.of([
[ id:'test', single_end:false, project: 'project' ], // meta map
file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
])
input[1] = GUNZIP.out.gunzip
input[2] = SAMTOOLS_FAIDX.out.fai
input[3] = "sniffles"
input[4] = [[],[]]
input[5] = Channel.of('chr20\t2650000\t2660000')
.collectFile(name: 'chr20.bed', newLine: true)
.map{ file -> [ [ id:'chr20'], file ] }
"""
}
}
Expand All @@ -312,7 +424,7 @@ nextflow_workflow {

}

test("2 samples - [bam, bai], fasta, fai, [] - sniffles -stub") {
test("2 samples - [bam, bai], fasta, fai, [], [] - sniffles -stub") {

options "-stub"

Expand All @@ -335,6 +447,7 @@ nextflow_workflow {
input[2] = SAMTOOLS_FAIDX.out.fai
input[3] = "sniffles"
input[4] = [[],[]]
input[5] = [[],[]]
"""
}
}
Expand All @@ -354,7 +467,37 @@ nextflow_workflow {

}

test("1 sample - [bam, bai], fasta, fai, [] - severus -stub") {
test("1 sample - [bam, bai], fasta, fai, [], [] - severus -stub") {

options "-stub"

when {
workflow {
"""
input[0] = Channel.of([
[ id:'test', single_end:false, project: 'project' ], // meta map
file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
])
input[1] = GUNZIP.out.gunzip
input[2] = SAMTOOLS_FAIDX.out.fai
input[3] = "severus"
input[4] = [[],[]]
input[5] = [[],[]]
"""
}
}

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

}

test("1 sample - [bam, bai], fasta, fai, [], bed - severus -stub") {

options "-stub"

Expand All @@ -370,6 +513,9 @@ nextflow_workflow {
input[2] = SAMTOOLS_FAIDX.out.fai
input[3] = "severus"
input[4] = [[],[]]
input[5] = Channel.of('chr20\t2650000\t2660000')
.collectFile(name: 'chr20.bed', newLine: true)
.map{ file -> [ [ id:'chr20'], file ] }
"""
}
}
Expand All @@ -383,7 +529,7 @@ nextflow_workflow {

}

test("1 sample - [bam, bai], fasta, fai, bed - severus -stub") {
test("1 sample - [bam, bai], fasta, fai, bed, [] - severus -stub") {

options "-stub"

Expand All @@ -402,6 +548,7 @@ nextflow_workflow {
[ id:'trf' ],
file('https://github.com/fritzsedlazeck/Sniffles/raw/master/annotations/human_GRCh38_no_alt_analysis_set.trf.bed', checkIfExists: true)
]
input[5] = [[],[]]
"""
}
}
Expand All @@ -415,7 +562,7 @@ nextflow_workflow {

}

test("2 samples - [bam, bai], fasta, fai, [] - severus -stub") {
test("2 samples - [bam, bai], fasta, fai, [], [] - severus -stub") {

options "-stub"

Expand All @@ -438,6 +585,7 @@ nextflow_workflow {
input[2] = SAMTOOLS_FAIDX.out.fai
input[3] = "severus"
input[4] = [[],[]]
input[5] = [[],[]]
"""
}
}
Expand Down
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