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fix and bump gfastats #7320

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fix and bump gfastats #7320

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553a546
fix and bump gfastats
fellen31 Jan 16, 2025
bd152dc
migrate pytest
fellen31 Jan 16, 2025
2754b3d
Merge branch 'master' into fix-gfastats
fellen31 Jan 16, 2025
8a67eb6
Update pytest_modules.yml
fellen31 Jan 16, 2025
8eb7df5
fix lint
fellen31 Jan 16, 2025
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2 changes: 1 addition & 1 deletion modules/nf-core/gfastats/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::gfastats=1.3.6
- bioconda::gfastats=1.3.9
24 changes: 12 additions & 12 deletions modules/nf-core/gfastats/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,18 +4,18 @@ process GFASTATS {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gfastats:1.3.6--hdcf5f25_3':
'biocontainers/gfastats:1.3.6--hdcf5f25_3' }"
'https://depot.galaxyproject.org/singularity/gfastats:1.3.9--h077b44d_1':
'biocontainers/gfastats:1.3.9--h077b44d_1' }"

input:
tuple val(meta), path(assembly) // input.[fasta|fastq|gfa][.gz]
val out_fmt // output format (fasta/fastq/gfa)
val genome_size // estimated genome size for NG* statistics (optional).
val target // target specific sequence by header, optionally with coordinates (optional).
path agpfile // -a --agp-to-path <file> converts input agp to path and replaces existing paths.
path include_bed // -i --include-bed <file> generates output on a subset list of headers or coordinates in 0-based bed format.
path exclude_bed // -e --exclude-bed <file> opposite of --include-bed. They can be combined (no coordinates).
path instructions // -k --swiss-army-knife <file> set of instructions provided as an ordered list.
tuple val(meta), path(assembly)
val out_fmt
val genome_size
val target
path agpfile
path include_bed
path exclude_bed
path instructions

output:
tuple val(meta), path("*.assembly_summary"), emit: assembly_summary
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Suggested change
tuple val(meta), path("*.assembly_summary"), emit: assembly_summary
tuple val(meta), path("*.assembly_summary"), emit: assembly_summary
tuple val(meta), path("*.${out_fmt}.gz") , emit: assembly, optional: true

something like this

Expand All @@ -28,7 +28,7 @@ process GFASTATS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def agp = agpfile ? "--agp-to-path $agp" : ""
def agp = agpfile ? "--agp-to-path $agpfile" : ""
def ibed = include_bed ? "--include-bed $include_bed" : ""
def ebed = exclude_bed ? "--exclude-bed $exclude_bed" : ""
def sak = instructions ? "--swiss-army-knife $instructions" : ""
Expand All @@ -55,7 +55,7 @@ process GFASTATS {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.${out_fmt}.gz
echo | gzip > ${prefix}.${out_fmt}.gz
touch ${prefix}.assembly_summary

cat <<-END_VERSIONS > versions.yml
Expand Down
314 changes: 314 additions & 0 deletions modules/nf-core/gfastats/tests/main.nf.test
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@@ -0,0 +1,314 @@
nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "gfastats"

test("test_gfastats_fasta_gfa") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = 'gfa' // GFA output format
input[2] = '' // No genome size
input[3] = '' // No target
input[4] = [] // No agp file
input[5] = [] // No include bed file
input[6] = [] // No exclude bed file
input[7] = [] // No swiss army knife instructions
"""
}
}

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

}

test("test_gfastats_gfa_fasta") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = 'fasta' // Fasta output format
input[2] = '' // No genome size
input[3] = '' // No target
input[4] = [] // No agp file
input[5] = [] // No include bed file
input[6] = [] // No exclude bed file
input[7] = [] // No swiss army knife instructions
"""
}
}

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

}

test("test_gfastats_include_bed") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = 'fastq' // Fastq output format
input[2] = '' // No genome size
input[3] = '' // No target
input[4] = [] // No agp file
input[5] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
input[6] = [] // No exclude bed file
input[7] = [] // No swiss army knife instructions
"""
}
}

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

}

test("test_gfastats_exclude_bed") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = 'fasta' // Fasta output format
input[2] = '' // No genome size
input[3] = '' // No target
input[4] = [] // No agp file
input[5] = [] // No include bed file
input[6] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
input[7] = [] // No swiss army knife instructions
"""
}
}

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

}

test("test_gfastats_sak") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = 'fasta' // Fasta output format
input[2] = '' // No genome size
input[3] = '' // No target
input[4] = [] // No agp file
input[5] = [] // No include bed file
input[6] = [] // No exclude bed file
input[7] = Channel.of(
'RVCP\tMT192765.1'
).collectFile(name:'assembly.sak')
"""
}
}

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

}

test("test_gfastats_fasta_gfa - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = 'gfa' // GFA output format
input[2] = '' // No genome size
input[3] = '' // No target
input[4] = [] // No agp file
input[5] = [] // No include bed file
input[6] = [] // No exclude bed file
input[7] = [] // No swiss army knife instructions
"""
}
}

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

}

test("test_gfastats_gfa_fasta - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = 'fasta' // Fasta output format
input[2] = '' // No genome size
input[3] = '' // No target
input[4] = [] // No agp file
input[5] = [] // No include bed file
input[6] = [] // No exclude bed file
input[7] = [] // No swiss army knife instructions
"""
}
}

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

}

test("test_gfastats_include_bed - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = 'fastq' // Fastq output format
input[2] = '' // No genome size
input[3] = '' // No target
input[4] = [] // No agp file
input[5] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
input[6] = [] // No exclude bed file
input[7] = [] // No swiss army knife instructions
"""
}
}

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

}

test("test_gfastats_exclude_bed - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = 'fasta' // Fasta output format
input[2] = '' // No genome size
input[3] = '' // No target
input[4] = [] // No agp file
input[5] = [] // No include bed file
input[6] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
input[7] = [] // No swiss army knife instructions
"""
}
}

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

}

test("test_gfastats_sak - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = 'fasta' // Fasta output format
input[2] = '' // No genome size
input[3] = '' // No target
input[4] = [] // No agp file
input[5] = [] // No include bed file
input[6] = [] // No exclude bed file
input[7] = Channel.of(
'RVCP\tMT192765.1'
).collectFile(name:'assembly.sak')
"""
}
}

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

}
}
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