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Merged
vagkaratzas merged 3 commits into from
Dec 17, 2025
Merged

Update cmaple #9580

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0bb6014
adding uncompression functionality
vagkaratzas Dec 17, 2025
f11fb71
new versions output syntax
vagkaratzas Dec 17, 2025
b5703f5
meta.yml updated
vagkaratzas Dec 17, 2025
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25 changes: 10 additions & 15 deletions modules/nf-core/cmaple/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,27 +13,27 @@ process CMAPLE {
output:
tuple val(meta), path("*.treefile"), emit: treefile
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
tuple val("${task.process}"), val("cmaple"), eval('cmaple --help | grep -m1 -oE "[0-9]+(\\.[0-9]+)+"'), topic: versions, emit: versions_cmaple

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

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def tree_arg = newick ? "-t ${newick}" : ""
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def is_compressed = aln.getExtension() == "gz"
def aln_name = is_compressed ? aln.getBaseName() : aln
def uncompress_input = is_compressed ? "gzip -c -d ${aln} > ${aln_name}" : ''
def tree_arg = newick ? "-t ${newick}" : ""
"""
$uncompress_input

cmaple-aa \\
$args \\
-nt $task.cpus \\
--prefix ${prefix} \\
${tree_arg} \\
-aln $aln

cat <<-END_VERSIONS > versions.yml
"${task.process}":
cmaple: \$(cmaple --help | grep -m1 'CMAPLE version' | sed -E 's/.*version ([0-9.]+).*/\\1/')
END_VERSIONS
-aln $aln_name
"""

stub:
Expand All @@ -44,10 +44,5 @@ process CMAPLE {

touch ${prefix}.treefile
touch ${prefix}.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
cmaple: \$(cmaple --help | grep -m1 'CMAPLE version' | sed -E 's/.*version ([0-9.]+).*/\\1/')
END_VERSIONS
"""
}
38 changes: 30 additions & 8 deletions modules/nf-core/cmaple/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,15 @@ input:
e.g. `[ id:'sample1', single_end:false ]`
- aln:
type: file
description: Multiple sequence alignment file in FASTA, PHYLIP, or MAPLE format
pattern: "*.{fa,fasta,faa,fna,fas,aln,afa,phy,phylip,maple}"
description: |
Multiple sequence alignment file in FASTA, PHYLIP, or MAPLE format.
Can be gzipped on uncompressed.
pattern: "*.{fa,fasta,faa,fna,fas,aln,afa,phy,phylip,maple}{.gz,}"
ontologies:
- edam: http://edamontology.org/data_0863 # Sequence alignment
- edam: http://edamontology.org/format_1929 # FASTA
- edam: http://edamontology.org/format_1997 # PHYLIP format
- edam: http://edamontology.org/format_3989 # GZIP format
- newick:
type: file
description: A Newick formatted tree based on multiple sequence alignment
Expand Down Expand Up @@ -68,13 +75,28 @@ output:
ontologies:
- edam: "http://edamontology.org/format_2330" # Textual format

versions_cmaple:
- - ${task.process}:
type: string
description: The name of the process
- cmaple:
type: string
description: The name of the tool
- cmaple --help | grep -m1 -oE "[0-9]+(\.[0-9]+)+":
type: eval
description: The expression to obtain the version of the tool

topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The name of the process
- cmaple:
type: string
description: The name of the tool
- cmaple --help | grep -m1 -oE "[0-9]+(\.[0-9]+)+":
type: eval
description: The expression to obtain the version of the tool

authors:
- "@vagkaratzas"
Expand Down
39 changes: 14 additions & 25 deletions modules/nf-core/cmaple/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,6 @@ nextflow_process {
tag "modules"
tag "modules_nfcore"
tag "cmaple"
tag "gunzip"

test("seatoxin - aa - aln") {

Expand All @@ -27,39 +26,25 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.log[0][1]).name,
process.out.treefile,
process.out.versions.collect{ path(it).yaml }
file(process.out.log[0][1]).name,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
}

}

test("haemophilus_influenzae - dna - newick - aln") {

setup {
run("GUNZIP") {
script "../../gunzip/main.nf"
process {
"""
input[0] = [
[ id: 'test_gunzip' ],
file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz', checkIfExists: true)
]
"""
}
}
}
test("haemophilus_influenzae - dna - newick - aln.gz") {

when {
process {
"""
input[0] = GUNZIP.out.gunzip.map{[
input[0] = [
[ id: 'test_dna' ],
it[1],
file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk', checkIfExists: true)
]}
]
"""
}
}
Expand All @@ -68,9 +53,9 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.log[0][1]).name,
process.out.treefile,
process.out.versions.collect{ path(it).yaml }
file(process.out.log[0][1]).name,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
}
Expand All @@ -96,8 +81,12 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out.versions).match("versions") }
{ assert snapshot(
process.out.treefile,
process.out.log,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() },

)
}

Expand Down
127 changes: 52 additions & 75 deletions modules/nf-core/cmaple/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,113 +1,90 @@
{
"seatoxin - aa - aln - stub": {
"content": [
[
[
{
"id": "test_stub"
},
"test_stub.treefile:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
[
{
"id": "test_stub"
},
"test_stub.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
{
"0": [
[
{
"id": "test_stub"
},
"test_stub.treefile:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test_stub"
},
"test_stub.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
"versions.yml:md5,975773bfb5d2679d2d0a78e1c5e1444a"
],
"log": [
"versions_cmaple": [
[
{
"id": "test_stub"
},
"test_stub.log:md5,d41d8cd98f00b204e9800998ecf8427e"
"CMAPLE",
"cmaple",
"1.1.0"
]
],
"treefile": [
[
{
"id": "test_stub"
},
"test_stub.treefile:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,975773bfb5d2679d2d0a78e1c5e1444a"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
"nextflow": "25.10.2"
},
"timestamp": "2025-10-16T13:44:33.656447134"
"timestamp": "2025-12-17T09:47:20.755458285"
},
"haemophilus_influenzae - dna - newick - aln": {
"seatoxin - aa - aln": {
"content": [
"test_dna.log",
[
[
{
"id": "test_dna"
"id": "test_aa"
},
"test_dna.treefile:md5,bbc5f987e523bda0335ae7a2d70b982c"
"test_aa.treefile:md5,e8d45477e64ac8aae9ebda4859acdaf1"
]
],
[
{
"CMAPLE": {
"cmaple": "1.1.0"
}
}
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
},
"timestamp": "2025-10-16T13:44:26.501246515"
},
"versions": {
"content": [
[
"versions.yml:md5,975773bfb5d2679d2d0a78e1c5e1444a"
]
"test_aa.log",
{
"versions_cmaple": [
[
"CMAPLE",
"cmaple",
"1.1.0"
]
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
"nextflow": "25.10.2"
},
"timestamp": "2025-10-16T13:44:33.677485714"
"timestamp": "2025-12-17T09:47:03.948254024"
},
"seatoxin - aa - aln": {
"haemophilus_influenzae - dna - newick - aln.gz": {
"content": [
"test_aa.log",
[
[
{
"id": "test_aa"
"id": "test_dna"
},
"test_aa.treefile:md5,e8d45477e64ac8aae9ebda4859acdaf1"
"test_dna.treefile:md5,bbc5f987e523bda0335ae7a2d70b982c"
]
],
[
{
"CMAPLE": {
"cmaple": "1.1.0"
}
}
]
"test_dna.log",
{
"versions_cmaple": [
[
"CMAPLE",
"cmaple",
"1.1.0"
]
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
"nextflow": "25.10.2"
},
"timestamp": "2025-10-16T13:44:18.090278163"
"timestamp": "2025-12-17T09:47:12.9837875"
}
}
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