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add tests for fq2bam #6902

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merged 4 commits into from
Oct 30, 2024
Merged

add tests for fq2bam #6902

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277cc53
add tests for fq2bam
sateeshperi Oct 29, 2024
0e7198e
Added tests for PE and stub
GallVp Oct 30, 2024
5f5a993
Fixed linting
GallVp Oct 30, 2024
2a4952f
Removed pytests
GallVp Oct 30, 2024
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6 changes: 6 additions & 0 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -644,6 +644,12 @@ jobs:
path: modules/nf-core/parabricks/fq2bammeth
- profile: singularity
path: modules/nf-core/parabricks/fq2bammeth
- profile: conda
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path: modules/nf-core/parabricks/fq2bam
- profile: docker_self_hosted
path: modules/nf-core/parabricks/fq2bam
- profile: singularity
path: modules/nf-core/parabricks/fq2bam
- profile: conda
path: subworkflows/nf-core/vcf_annotate_ensemblvep
- profile: conda
Expand Down
37 changes: 14 additions & 23 deletions modules/nf-core/parabricks/fq2bam/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,21 +2,22 @@ process PARABRICKS_FQ2BAM {
tag "$meta.id"
label 'process_high'

container "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1"
container "nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1"

input:
tuple val(meta), path(reads), path(interval_file)
tuple val(meta), path(reads)
tuple val(meta2), path(fasta)
tuple val(meta3), path(index)
path known_sites
path(interval_file)
path(known_sites)

output:
tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*.bai") , emit: bai
path "versions.yml" , emit: versions
path "qc_metrics", optional:true , emit: qc_metrics
path("*.table"), optional:true , emit: bqsr_table
path("duplicate-metrics.txt"), optional:true , emit: duplicate_metrics
tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*.bai") , emit: bai
path "versions.yml" , emit: versions
path "qc_metrics" , emit: qc_metrics , optional:true
path("*.table") , emit: bqsr_table , optional:true
path("duplicate-metrics.txt") , emit: duplicate_metrics , optional:true

when:
task.ext.when == null || task.ext.when
Expand All @@ -32,21 +33,20 @@ process PARABRICKS_FQ2BAM {
def known_sites_command = known_sites ? known_sites.collect{"--knownSites $it"}.join(' ') : ""
def known_sites_output = known_sites ? "--out-recal-file ${prefix}.table" : ""
def interval_file_command = interval_file ? interval_file.collect{"--interval-file $it"}.join(' ') : ""
def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
"""

INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
mv $fasta \$INDEX
cp $fasta \$INDEX

pbrun \\
fq2bam \\
--ref \$INDEX \\
$in_fq_command \\
--read-group-sm $meta.id \\
--out-bam ${prefix}.bam \\
$known_sites_command \\
$known_sites_output \\
$interval_file_command \\
--num-gpus $task.accelerator.request \\
$num_gpus \\
$args

cat <<-END_VERSIONS > versions.yml
Expand All @@ -62,19 +62,10 @@ process PARABRICKS_FQ2BAM {
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def in_fq_command = meta.single_end ? "--in-se-fq $reads" : "--in-fq $reads"
def known_sites_command = known_sites ? known_sites.collect{"--knownSites $it"}.join(' ') : ""
def known_sites_output = known_sites ? "--out-recal-file ${prefix}.table" : ""
def interval_file_command = interval_file ? interval_file.collect{"--interval-file $it"}.join(' ') : ""
def metrics_output_command = args = "--out-duplicate-metrics duplicate-metrics.txt" ? "touch duplicate-metrics.txt" : ""
def known_sites_output_command = known_sites ? "touch ${prefix}.table" : ""
def qc_metrics_output_command = args = "--out-qc-metrics-dir qc_metrics " ? "mkdir qc_metrics && touch qc_metrics/alignment.txt" : ""
"""
touch ${prefix}.bam
touch ${prefix}.bam.bai
$metrics_output_command
$known_sites_output_command
$qc_metrics_output_command

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pbrun: \$(echo \$(pbrun version 2>&1) | sed 's/^Please.* //' )
Expand Down
11 changes: 6 additions & 5 deletions modules/nf-core/parabricks/fq2bam/meta.yml
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Expand Up @@ -24,11 +24,6 @@ input:
type: file
description: fastq.gz files
pattern: "*.fastq.gz"
- interval_file:
type: file
description: (optional) file(s) containing genomic intervals for use in base
quality score recalibration (BQSR)
pattern: "*.{bed,interval_list,picard,list,intervals}"
- - meta2:
type: map
description: |
Expand All @@ -45,6 +40,11 @@ input:
type: file
description: reference BWA index
pattern: "*.{amb,ann,bwt,pac,sa}"
- - interval_file:
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type: file
description: (optional) file(s) containing genomic intervals for use in base
quality score recalibration (BQSR)
pattern: "*.{bed,interval_list,picard,list,intervals}"
- - known_sites:
type: file
description: (optional) known sites file(s) for calculating BQSR. markdups must
Expand Down Expand Up @@ -99,3 +99,4 @@ authors:
maintainers:
- "@bsiranosian"
- "@adamrtalbot"
- "@gallvp"
174 changes: 174 additions & 0 deletions modules/nf-core/parabricks/fq2bam/tests/main.nf.test
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@@ -0,0 +1,174 @@
nextflow_process {

name "Test Process PARABRICKS_FQ2BAM"
script "../main.nf"
process "PARABRICKS_FQ2BAM"
config "./nextflow.config"

tag "bwa/index"
tag "modules"
tag "parabricks/fq2bam"
tag "modules_nfcore"
tag "parabricks"

setup {
run("BWA_INDEX") {
script "../../../bwa/index/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test' ], // meta map
file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
])
"""
}
}

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

test("SRR389222 - fastq - se") {

when {
process {
"""
input[0] = Channel.of([
[ id:'test', single_end:true ], // meta map
[
file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
]
])
input[1] = Channel.of([
[ id:'test' ], // meta map
file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
])
input[2] = BWA_INDEX.out.index
input[3] = []
input[4] = []
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
bam(process.out.bam[0][1]).getReadsMD5(),
file(process.out.bai[0][1]).name,
process.out.versions
).match() }
)
}
}

test("SRR389222 - fastq - se - stub") {
options '-stub'

when {
process {
"""
input[0] = Channel.of([
[ id:'test', single_end:true ], // meta map
[
file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
]
])
input[1] = Channel.of([
[ id:'test' ], // meta map
file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
])
input[2] = BWA_INDEX.out.index
input[3] = []
input[4] = []
"""
}
}

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

test("sarscov2 - fastq - pe") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
]
]
input[1] = Channel.of([
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
])
input[2] = BWA_INDEX_PE.out.index
input[3] = []
input[4] = []
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
bam(process.out.bam[0][1]).getReadsMD5(),
file(process.out.bai[0][1]).name,
process.out.versions
).match() }
)
}

}

test("sarscov2 - fastq - pe - stub") {
options '-stub'

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
]
]
input[1] = Channel.of([
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
])
input[2] = BWA_INDEX_PE.out.index
input[3] = []
input[4] = []
"""
}
}

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

}

}
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