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correct president stub #5904

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merged 3 commits into from
Jul 2, 2024
Merged

correct president stub #5904

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fdbe1a7
correct president stub
paulwolk Jul 2, 2024
71d0a4e
Large update to module
SPPearce Jul 2, 2024
b1b0000
Update prefix and meta
SPPearce Jul 2, 2024
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34 changes: 19 additions & 15 deletions modules/nf-core/president/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,37 +9,38 @@ process PRESIDENT {

input:
tuple val(meta), path(fasta)
path reference
tuple val(meta2), path(reference)
val compress

output:
tuple val(meta), path("output/*.fasta*"), emit: fasta
tuple val(meta), path("output/*.tsv") , emit: report
tuple val(meta), path("output/*.log") , emit: log
path "versions.yml" , emit: versions
tuple val(meta), path("${prefix}valid.fasta*") , emit: valid_fasta
tuple val(meta), path("${prefix}invalid.fasta*"), emit: invalid_fasta
tuple val(meta), path("*.tsv") , emit: report
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: ''
if (prefix != ''){
prefix = "--prefix " + prefix
}

prefix = task.ext.prefix ?: "${meta.id}_"
if ("${fasta}" == "${reference}") error "Input and reference names are the same!"
if ("${fasta}" == "${prefix}valid.fasta") error "Input and output file names are the same, use \"task.ext.prefix\" to disambiguate!"
if ("${fasta}" == "${prefix}invalid.fasta") error "Input and output file names are the same, use \"task.ext.prefix\" to disambiguate!"
if ("${fasta}" == "${prefix}valid.fasta.gz" && compress) error "Input and output file names are the same, use \"task.ext.prefix\" to disambiguate!"
if ("${fasta}" == "${prefix}invalid.fasta.gz" && compress) error "Input and output file names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
mkdir output
president \\
--query $fasta \\
--reference $reference \\
--path output \\
--path . \\
--threads $task.cpus \\
$prefix \\
--prefix $prefix \\
$args

if [ "$compress" = true ] ; then
gzip output/*.fasta;
gzip ${prefix}*.fasta;
fi

cat <<-END_VERSIONS > versions.yml
Expand All @@ -50,12 +51,15 @@ process PRESIDENT {

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: ''
prefix = task.ext.prefix ?: "${meta.id}_"
compress_command = compress ? "gzip ${prefix}*.fasta" : ""

"""
touch ${prefix}report.tsv
touch ${prefix}president_logger.log
touch ${prefix}valid.fasta
touch ${prefix}invalid.fasta
$compress_command

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
3 changes: 3 additions & 0 deletions modules/nf-core/president/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,9 @@ input:
type: file
description: One fasta file or a list of multiple fasta files to perform president on. Has to be uncompressed!
pattern: "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}"
- meta2:
type: map
description: Groovy Map containing information about the reference genome
- reference:
type: file
description: Fasta of a reference genome. Has to be uncompressed!
Expand Down
99 changes: 69 additions & 30 deletions modules/nf-core/president/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,12 @@ nextflow_process {

when {
process {
"""
input[0] = [[],file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true)]
input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
"""
input[0] = [
[id: "test" ],
file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true)
]
input[1] = [[id: "genome" ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
input[2] = []
"""

Expand All @@ -32,22 +35,16 @@ nextflow_process {

assertAll(
{assert process.success},
{assert snapshot(process.out.versions,
process.out.valid_fasta,
process.out.invalid_fasta).match()},
{assert process.out.log != null},
{assert process.out.log.size() == 1},
{assert process.out.log.get(0).get(1) ==~ ".*/president_logger.log"},
{assert process.out.log.get(0).get(1) ==~ ".*president_logger.log"},
{assert process.out.report != null},
{assert process.out.report.size() == 1},
{assert process.out.report.get(0).get(1) ==~ ".*/report.tsv"},
{assert process.out.report.get(0).get(1) ==~ ".*report.tsv"},
{assert firstReportEntry == firstReportAssert},
{assert process.out.fasta != null},
{assert process.out.fasta.size() == 1},
{assert process.out.fasta.get(0).get(1).size() == 2},
{assert process.out.fasta.get(0).get(1).get(0) ==~ ".*/invalid.fasta"},
{assert path(process.out.fasta.get(0).get(1).get(0)).readLines().size() == 2},
{assert path(process.out.fasta.get(0).get(1).get(0)).md5 == "5e16f45d529bac4c6d757a84802ac772"},
{assert process.out.fasta.get(0).get(1).get(1) ==~ ".*/valid.fasta"},
{assert path(process.out.fasta.get(0).get(1).get(1)).readLines().size() == 6},
{assert path(process.out.fasta.get(0).get(1).get(1)).md5 == "16031b5d95fff7ff01b60615728df4ab"}
)
}
}
Expand All @@ -56,9 +53,12 @@ nextflow_process {

when {
process {
"""
input[0] = [[],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true)]
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
"""
input[0] = [
[id: "test" ],
file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true)
]
input[1] = [[id: "genome" ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
input[2] = "true"
"""
}
Expand All @@ -73,28 +73,67 @@ nextflow_process {
firstReportAssert.add(sdf.format(date))
assertAll(
{assert process.success},

{assert snapshot(process.out.versions,
process.out.valid_fasta,
process.out.invalid_fasta).match()},
{assert process.out.log != null},
{assert process.out.log.size() == 1},
{assert process.out.log.get(0).get(1) ==~ ".*/president_logger.log"},
{assert process.out.log.get(0).get(1) ==~ ".*president_logger.log"},

{assert process.out.report != null},
{assert process.out.report.size() == 1},
{assert process.out.report.get(0).get(1) ==~ ".*/report.tsv"},

{assert process.out.report.get(0).get(1) ==~ ".*report.tsv"},
{assert firstReportEntry == firstReportAssert},
)
}
}

{assert process.out.fasta != null},
{assert process.out.fasta.size() == 1},
{assert process.out.fasta.get(0).get(1).size() == 2},
{assert process.out.fasta.get(0).get(1).get(0) ==~ ".*/invalid.fasta.gz"},
{assert path(process.out.fasta.get(0).get(1).get(0)).linesGzip.size() == 2},
{assert path(process.out.fasta.get(0).get(1).get(0)).md5 == "5e16f45d529bac4c6d757a84802ac772"},
test("president - nocompress - stub") {
options "-stub"
when {
process {
"""
input[0] = [
[id: "test" ],
file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true)
]
input[1] = [[id: "genome" ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
input[2] = false
"""

}
}

{assert process.out.fasta.get(0).get(1).get(1) ==~ ".*/valid.fasta.gz"},
{assert path(process.out.fasta.get(0).get(1).get(1)).linesGzip.size() == 6},
{assert path(process.out.fasta.get(0).get(1).get(1)).md5 == "16031b5d95fff7ff01b60615728df4ab"}
then {
assertAll(
{assert process.success},
{assert snapshot(process.out).match()}
)
}
}

test("president - compress - stub") {
options "-stub"
when {
process {
"""
input[0] = [
[id: "test" ],
file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true)
]
input[1] = [[id: "genome" ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
input[2] = true
"""

}
}

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

}
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