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Pytest -> Nftest Readwriter #6077

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merged 10 commits into from
Aug 1, 2024
Merged

Pytest -> Nftest Readwriter #6077

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cf2edbb
migarte test files
FriederikeHanssen Jul 31, 2024
a60fd09
pytest to nftest for sentieon/readwriter
FriederikeHanssen Aug 1, 2024
af305a3
test out simple string syntax
FriederikeHanssen Aug 1, 2024
34a8b78
fasta in meta
FriederikeHanssen Aug 1, 2024
5c0c70c
check cram files by matching header and readmd5 sums
FriederikeHanssen Aug 1, 2024
8ba4fc7
remove header check because conda uses a different CL tag
FriederikeHanssen Aug 1, 2024
65e8d42
Merge branch 'master' into nftest_readwriter
FriederikeHanssen Aug 1, 2024
5ad99c6
fix channel cardinality for merge test
FriederikeHanssen Aug 1, 2024
e185f6f
Merge remote-tracking branch 'origin' into nftest_readwriter
FriederikeHanssen Aug 1, 2024
eed8941
Merge branch 'nftest_readwriter' of https://github.com/nf-core/module…
FriederikeHanssen Aug 1, 2024
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31 changes: 16 additions & 15 deletions modules/nf-core/sentieon/readwriter/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,10 +14,10 @@ process SENTIEON_READWRITER {
tuple val(meta3), path(fai)

output:
tuple val(meta), path("*.${format}"), emit: output
tuple val(meta), path("*.${index}") , emit: index
tuple val(meta), path("*.${format}"), path("*.${index}"), emit: output_index
path "versions.yml" , emit: versions
tuple val(meta), path("${prefix}"), emit: output
tuple val(meta), path("${prefix}.${index}"), emit: index
tuple val(meta), path("${prefix}"), path("${prefix}.${index}"), emit: output_index
path "versions.yml", emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -27,11 +27,15 @@ process SENTIEON_READWRITER {

def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def input_str = input.sort().collect{"-i $it"}.join(' ')
def input_str = input.sort{ it.getName() }.collect{"-i $it"}.join(' ')
def reference = fasta ? "-r $fasta" : ''
def prefix = task.ext.prefix ?: "${meta.id}"
format = input.extension == "bam" ? "bam" : "cram"
index = format == "bam" ? "bam.bai" : "cram.crai"

// bam -> bam: prefix = "<filename>.bam"
// bam -> cram: prefix = "<filename>.cram"
// cram -> cram: prefix = "<filename>.cram"
prefix = task.ext.prefix ?: "${meta.id}.bam"
index = prefix.tokenize('.')[-1] == "bam" ? "bai" : "crai"

def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ?
"export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " :
""
Expand All @@ -46,7 +50,7 @@ process SENTIEON_READWRITER {
$input_str \\
--algo ReadWriter \\
$args2 \\
${prefix}.${format}
${prefix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -55,14 +59,11 @@ process SENTIEON_READWRITER {
"""

stub:


def prefix = task.ext.prefix ?: "${meta.id}"
format = input.extension == "bam" ? "bam" : "cram"
index = format == "bam" ? "bam.bai" : "cram.crai"
prefix = task.ext.prefix ?: "${meta.id}.cram"
index = prefix.tokenize('.')[-1] == "bam" ? "bai" : "crai"
"""

touch ${prefix}.${format}
touch ${prefix}
touch ${prefix}.${index}

cat <<-END_VERSIONS > versions.yml
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/sentieon/readwriter/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ output:
e.g. [ id:'test', single_end:false ]
- output:
type: file
description: BAM/CRAM file
description: BAM/CRAM file. Depends on how ext.prefix is set. BAM "ext.prefix = <filename>.bam", CRAM "ext.prefix = <filename>.cram". Defaults to cram
pattern: "*.{bam,cram}"
- index:
type: file
Expand Down
173 changes: 173 additions & 0 deletions modules/nf-core/sentieon/readwriter/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -0,0 +1,173 @@
nextflow_process {

name "Test Process SENTIEON_READWRITER"
script "../main.nf"
process "SENTIEON_READWRITER"

tag "modules"
tag "modules_nfcore"
tag "sentieon"
tag "sentieon/readwriter"

test("merge bam") {
config "./nextflow.config"

when {
process {
"""
input[0] = [ [id: 'test' ],
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] = [[:],[]]
input[2] = [[:],[]]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
bam(process.out.output[0][1], stringency: "lenient").getReadsMD5(),
bam(process.out.output[0][1], stringency: "lenient").getHeader(),
file(process.out.index.get(0).get(1)).name,
process.out.versions
).match() }

)
}

}

test("cram") {
config "./nextflow_outputcram.config"
when {
process {
"""
input[0] = [ [id: 'test', fasta: params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta' ],
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)
]
input[1] = [ [ id:'fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
input[2] = [ [ id:'fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
bam(process.out.output[0][1], process.out.output[0][0].fasta).getReadsMD5(),
bam(process.out.output[0][1], process.out.output[0][0].fasta).getHeader(),
file(process.out.index.get(0).get(1)).name,
process.out.versions
).match() }

)
}
}

test("merging - output bam") {
config "./nextflow.config"

when {
process {
"""
input[0] = [ [id: 'test' ],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
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.single_end.sorted.bam', checkIfExists: true)
],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', 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/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
],
[]
]
input[1] = [[:],[]]
input[2] = [[:],[]]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
bam(process.out.output[0][1], stringency: "lenient").getReadsMD5(),
bam(process.out.output[0][1], stringency: "lenient").getHeader(),
file(process.out.index.get(0).get(1)).name,
process.out.versions
).match() }

)
}

}

test("merging - output bam to cram") {
config "./nextflow_outputcram.config"

when {
process {
"""
input[0] = [ [id: 'test', fasta: params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta' ],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
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.single_end.sorted.bam', checkIfExists: true)
],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', 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/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
]
]
input[1] = [ [ id:'fasta' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
input[2] = [ [ id:'fasta' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
bam(process.out.output[0][1], process.out.output[0][0].fasta).getReadsMD5(),
bam(process.out.output[0][1], process.out.output[0][0].fasta).getHeader(),
file(process.out.index.get(0).get(1)).name,
process.out.versions
).match() }

)
}

}

test("sentieon readwriter - stub") {
options "-stub"
config "./nextflow.config"

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)
]
input[1] = [ [ id:'fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
input[2] = [ [ id:'fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
"""
}
}

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

}

}
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