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index should be emitted as either tbi or csi #7385

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index should be emitted as either tbi or csi #7385

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69b9397
index should be emitted as either tbi or csi
tkchafin Jan 28, 2025
b5dd005
Merge branch 'master' into tkchafin-patch-1
tkchafin Jan 28, 2025
093d197
Merge branch 'master' into tkchafin-patch-1
famosab Feb 6, 2025
05420ff
Merge branch 'master' into tkchafin-patch-1
SPPearce Mar 7, 2025
71ed27d
Merge branch 'master' into tkchafin-patch-1
famosab Mar 12, 2025
b24e0e7
update meta
famosab Mar 12, 2025
fbdfb3f
Merge branch 'tkchafin-patch-1' of https://github.com/nf-core/modules…
famosab Mar 12, 2025
7c5af98
update tests
famosab Mar 12, 2025
3af3e5f
snaps but gzipped ones fail
famosab Mar 12, 2025
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10 changes: 5 additions & 5 deletions modules/nf-core/deepvariant/rundeepvariant/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,11 +16,11 @@ process DEEPVARIANT_RUNDEEPVARIANT {
tuple val(meta5), path(par_bed)

output:
tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf
tuple val(meta), path("${prefix}.vcf.gz.tbi") , emit: vcf_tbi
tuple val(meta), path("${prefix}.g.vcf.gz") , emit: gvcf
tuple val(meta), path("${prefix}.g.vcf.gz.tbi"), emit: gvcf_tbi
path "versions.yml" , emit: versions
tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf
tuple val(meta), path("${prefix}.vcf.gz.{tbi,csi}") , emit: vcf_index
tuple val(meta), path("${prefix}.g.vcf.gz") , emit: gvcf
tuple val(meta), path("${prefix}.g.vcf.gz.{tbi,csi}") , emit: gvcf_index
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand Down
12 changes: 6 additions & 6 deletions modules/nf-core/deepvariant/rundeepvariant/meta.yml
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Expand Up @@ -79,16 +79,16 @@ output:
type: file
description: Compressed VCF file
pattern: "*.vcf.gz"
- vcf_tbi:
- vcf_index:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- ${prefix}.vcf.gz.tbi:
- ${prefix}.vcf.gz.{tbi,csi}:
type: file
description: Tabix index file of compressed VCF
pattern: "*.vcf.gz.tbi"
pattern: "*.vcf.gz.{tbi,csi}"
- gvcf:
- meta:
type: map
Expand All @@ -99,16 +99,16 @@ output:
type: file
description: Compressed GVCF file
pattern: "*.g.vcf.gz"
- gvcf_tbi:
- gvcf_index:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- ${prefix}.g.vcf.gz.tbi:
- ${prefix}.g.vcf.gz.{tbi,csi}:
type: file
description: Tabix index file of compressed GVCF
pattern: "*.g.vcf.gz.tbi"
pattern: "*.g.vcf.gz.{tbi,csi}"
- versions:
- versions.yml:
type: file
Expand Down
106 changes: 100 additions & 6 deletions modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test
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Expand Up @@ -8,11 +8,14 @@ nextflow_process {
tag "deepvariant"
tag "modules"
tag "modules_nfcore"
config "./nextflow.config"

test("homo_sapiens - [bam, bai] - fasta - fai") {
when {
config "./nextflow.config"

when {
params {
module_args = '--regions=\"chr22:0-40001\" --model_type=WGS'
}
process {
"""
input[0] = [
Expand Down Expand Up @@ -48,9 +51,11 @@ nextflow_process {
}

test("homo_sapiens - [cram, crai, genome_bed] - fasta - fai") {
config "./nextflow-intervals.config"

when {
params {
module_args = '--model_type=WGS'
}
process {
"""
input[0] = [
Expand Down Expand Up @@ -86,9 +91,11 @@ nextflow_process {
}

test("homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_bed") {
config "./nextflow-non-autosomal-calling.config"
tag "test"

when {
params {
module_args = '--model_type=WGS --haploid_contigs chr22'
}
process {
"""
input[0] = [
Expand Down Expand Up @@ -125,9 +132,96 @@ nextflow_process {
}

test("homo_sapiens - [bam, bai] - fasta_gz - fasta_gz_fai") {

when {
params {
module_args = ''
}
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
[]
]
input[1] = [
[ id:'genome'],
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true)
]
input[2] = [
[ id:'genome'],
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true)
]
input[3] = [
[ id:'genome'],
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz.gzi', checkIfExists: true)
]
input[4] = [
[],[]
]
"""
}
}

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

test("homo_sapiens - [bam, bai] - fasta - fai - stub") {

options "-stub"

when {
config "./nextflow.config"
params {
module_args = ''
}
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
[]
]
input[1] = [
[ id:'genome'],
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
]
input[2] = [
[ id:'genome'],
file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
input[3] = [
[],[]
]
input[4] = [
[],[]
]
"""
}
}

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

test("homo_sapiens - [bam, bai] - fasta_gz - fasta_gz_fai - stub") {

options "-stub"

when {
params {
module_args = ''
}
process {
"""
input[0] = [
Expand Down
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