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Provide .fna support for pbmm2/align #12602

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9576397
add fna support for pbmm2
stvdsomp Jul 31, 2026
c4fb517
add .fna support for pbmm2/align + test
stvdsomp Aug 6, 2026
36c4229
remove duplicate stub testing
stvdsomp Aug 6, 2026
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13 changes: 12 additions & 1 deletion modules/nf-core/pbmm2/align/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -23,10 +23,21 @@ process PBMM2_ALIGN {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
fasta="${fasta}"
if [[ \${fasta} == *.fna ]]; then
new_name=\${fasta%.fna}.fa
mv \${fasta} \${new_name}
fasta=\${new_name}
elif [[ \${fasta} == *.fna.gz ]]; then
new_name=\${fasta%.fna.gz}.fa.gz
mv \${fasta} \${new_name}
fasta=\${new_name}
fi

pbmm2 \\
align \\
$args \\
$fasta \\
\${fasta} \\
$bam \\
${prefix}.bam \\
--num-threads ${task.cpus}
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67 changes: 67 additions & 0 deletions modules/nf-core/pbmm2/align/tests/fna.nf.test
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@nvnieuwk nvnieuwk Aug 6, 2026

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Please add all tests to main.nf.test. This way all tests are in the same place which makes it easier to update them if necessary

Original file line number Diff line number Diff line change
@@ -0,0 +1,67 @@
nextflow_process {

name "Test Process PBMM2_ALIGN"
script "../main.nf"
process "PBMM2_ALIGN"

tag "modules"
tag "modules_nfcore"
tag "pbmm2"
tag "pbmm2/align"

test("pbmm2 - bam - fna") {
when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
]

input[1] = [
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fna', checkIfExists: true),
]
"""
}
}

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

}

test("pbmm2 - bam - fna - stub") {

@nvnieuwk nvnieuwk Aug 6, 2026

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No need for a stub test here since there is already one in the main.nf.test


options "-stub"

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
]

input[1] = [
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fna', checkIfExists: true),
]
"""
}
}

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

}

}
54 changes: 54 additions & 0 deletions modules/nf-core/pbmm2/align/tests/fna.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -0,0 +1,54 @@
{
"pbmm2 - bam - fna": {
"content": [
{
"bam": [
[
{
"id": "test"
},
"test.bam:md5,f0f615a8a6172a739dfb81e6e08043f4"
]
],
"versions_pbmm2": [
[
"PBMM2_ALIGN",
"pbmm2",
"26.2.0"
]
]
}
],
"timestamp": "2026-08-06T11:28:10.82763057",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
},
"pbmm2 - bam - fna - stub": {
"content": [
{
"bam": [
[
{
"id": "test"
},
"test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions_pbmm2": [
[
"PBMM2_ALIGN",
"pbmm2",
"26.2.0"
]
]
}
],
"timestamp": "2026-08-06T11:28:15.998416537",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
}
}
6 changes: 3 additions & 3 deletions modules/nf-core/pbmm2/align/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
{
"id": "test"
},
"test.bam:md5,f2be1fe20bbccf66afae237452e112cd"
"test.bam:md5,ccb989e67933259d6213ca6236b7971c"
]
],
"versions_pbmm2": [
Expand All @@ -19,10 +19,10 @@
]
}
],
"timestamp": "2026-07-01T15:03:18.017362993",
"timestamp": "2026-07-31T11:02:25.18889907",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.03.4"
"nextflow": "26.04.6"
}
},
"pbmm2 - bam - stub": {
Expand Down