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add stubs gatk4 #6672

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merged 5 commits into from
Sep 25, 2024
Merged

add stubs gatk4 #6672

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6e2031e
add stubs
famosab Sep 20, 2024
5a0c433
run lint --fix
famosab Sep 20, 2024
0b5f9b8
Merge branch 'master' into gatk-stub
famosab Sep 20, 2024
d5c3412
fix formatting
famosab Sep 25, 2024
33165bf
Merge branch 'master' into gatk-stub
famosab Sep 25, 2024
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13 changes: 13 additions & 0 deletions modules/nf-core/gatk4/applybqsr/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -48,4 +48,17 @@ process GATK4_APPLYBQSR {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def input_extension = input.getExtension()
def output_extension = input_extension == 'bam' ? 'bam' : 'cram'
"""
touch ${prefix}.${output_extension}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}
101 changes: 55 additions & 46 deletions modules/nf-core/gatk4/applybqsr/meta.yml
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Expand Up @@ -16,56 +16,65 @@ tools:
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ["Apache-2.0"]
identifier: ""
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/CRAM file from alignment
pattern: "*.{bam,cram}"
- input_index:
type: file
description: BAI/CRAI file from alignment
pattern: "*.{bai,crai}"
- bqsr_table:
type: file
description: Recalibration table from gatk4_baserecalibrator
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/CRAM file from alignment
pattern: "*.{bam,cram}"
- input_index:
type: file
description: BAI/CRAI file from alignment
pattern: "*.{bai,crai}"
- bqsr_table:
type: file
description: Recalibration table from gatk4_baserecalibrator
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- - fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- - fai:
type: file
description: Index of reference fasta file
pattern: "*.fasta.fai"
- - dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: Recalibrated BAM file
pattern: "*.{bam}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- "*.bam":
type: file
description: Recalibrated BAM file
pattern: "*.{bam}"
- cram:
type: file
description: Recalibrated CRAM file
pattern: "*.{cram}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- "*.cram":
type: file
description: Recalibrated CRAM file
pattern: "*.{cram}"
- versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@yocra3"
- "@FriederikeHanssen"
Expand Down
59 changes: 59 additions & 0 deletions modules/nf-core/gatk4/applybqsr/tests/main.nf.test
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Expand Up @@ -92,4 +92,63 @@ nextflow_process {
}
}

test("sarscov2 - cram - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test' ],
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),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
]
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
"""
}
}

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

test("sarscov2 - bam - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test' ],
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),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true),
[]
]
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
"""
}
}

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

}

}
78 changes: 78 additions & 0 deletions modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,4 +1,43 @@
{
"sarscov2 - bam - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [

],
"2": [
"versions.yml:md5,bb2a060a0280c812fba3c74b1707b350"
],
"bam": [
[
{
"id": "test"
},
"test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"cram": [

],
"versions": [
"versions.yml:md5,bb2a060a0280c812fba3c74b1707b350"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-20T10:25:00.314573"
},
"sarscov2 - bam - intervals": {
"content": [
{
Expand Down Expand Up @@ -60,6 +99,45 @@
},
"timestamp": "2023-12-09T03:10:46.70859771"
},
"sarscov2 - cram - stub": {
"content": [
{
"0": [

],
"1": [
[
{
"id": "test"
},
"test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
"versions.yml:md5,bb2a060a0280c812fba3c74b1707b350"
],
"bam": [

],
"cram": [
[
{
"id": "test"
},
"test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,bb2a060a0280c812fba3c74b1707b350"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-20T10:24:52.761169"
},
"sarscov2 - bam": {
"content": [
{
Expand Down
18 changes: 18 additions & 0 deletions modules/nf-core/gatk4/collectsvevidence/main.nf
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Expand Up @@ -54,4 +54,22 @@ process GATK4_COLLECTSVEVIDENCE {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def sd_vcf = site_depth_vcf ? "echo '' | gzip > ${prefix}.sd.txt.gz" : ""
def sd_vcf_tbi = site_depth_vcf_tbi ? "touch ${prefix}.sd.txt.gz.tbi" : ""
"""
echo "" | gzip > ${prefix}.sr.txt.gz
touch ${prefix}.sr.txt.gz.tbi
echo "" | gzip > ${prefix}.pe.txt.gz
touch ${prefix}.pe.txt.gz.tbi
${sd_vcf}
${sd_vcf_tbi}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}
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