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Update to topics graphmap2/* #11596

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22 changes: 6 additions & 16 deletions modules/nf-core/graphmap2/align/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ process GRAPHMAP2_ALIGN {

output:
tuple val(meta), path("*.sam"), emit: sam
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('graphmap2'), eval("graphmap2 2>&1 | sed -n 's/Version: v//p'"), emit: versions_graphmap2, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -26,29 +26,19 @@ process GRAPHMAP2_ALIGN {
"""
graphmap2 \\
align \\
-t $task.cpus \\
-r $fasta \\
-i $index \\
-d $reads \\
-t ${task.cpus} \\
-r ${fasta} \\
-i ${index} \\
-d ${reads} \\
-o ${prefix}.sam \\
$args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
graphmap2: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
END_VERSIONS
${args}
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"

"""
touch ${prefix}.sam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
graphmap2: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
END_VERSIONS
"""

}
32 changes: 24 additions & 8 deletions modules/nf-core/graphmap2/align/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
name: graphmap2_align
description: A versatile pairwise aligner for genomic and spliced nucleotide sequences
description: A versatile pairwise aligner for genomic and spliced nucleotide
sequences
keywords:
- align
- fasta
Expand All @@ -12,7 +13,8 @@ tools:
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
homepage: https://github.com/lbcb-sci/graphmap2
documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads
licence: ["MIT"]
licence:
- "MIT"
identifier: biotools:Graphmap2
input:
- - meta:
Expand Down Expand Up @@ -46,13 +48,27 @@ output:
description: Alignment in SAM format
pattern: "*.sam"
ontologies: []
versions_graphmap2:
- - ${task.process}:
type: string
description: The name of the process
- graphmap2:
type: string
description: The name of the tool
- "graphmap2 2>&1 | sed -n 's/Version: v//p'":
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
- graphmap2:
type: string
description: The name of the tool
- "graphmap2 2>&1 | sed -n 's/Version: v//p'":
type: eval
description: The expression to obtain the version of the tool
authors:
- "@yuukiiwa"
- "@drpatelh"
Expand Down
15 changes: 4 additions & 11 deletions modules/nf-core/graphmap2/align/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ nextflow_process {
"""
input[0] = [
[id:'test'],
[file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists:true)]
file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists:true)
]
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists:true)
input[2] = GRAPHMAP2_INDEX.out.index
Expand All @@ -40,11 +40,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
// sam(process.out.sam[0][1]).getSamLinesMD5() htsjdk.samtools.SAMFormatException: Error parsing text SAM file. MAPQ must be zero if RNAME is not specified
file(process.out.sam[0][1]).name
).match() }
{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["sam"])).match() }
)
}
}
Expand All @@ -57,7 +53,7 @@ nextflow_process {
"""
input[0] = [
[id:'test'],
[file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists:true)]
file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists:true)
]
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists:true)
input[2] = GRAPHMAP2_INDEX.out.index
Expand All @@ -67,10 +63,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
59 changes: 30 additions & 29 deletions modules/nf-core/graphmap2/align/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,52 +2,53 @@
"sarscov2 - fastq - fasta - index -- stub": {
"content": [
{
"0": [
"sam": [
[
{
"id": "test"
},
"test.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,0c397959d073e21ab58ceed89978f8bb"
],
"sam": [
"versions_graphmap2": [
[
{
"id": "test"
},
"test.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
"GRAPHMAP2_ALIGN",
"graphmap2",
"0.6.3"
]
],
"versions": [
"versions.yml:md5,0c397959d073e21ab58ceed89978f8bb"
]
},
{
"GRAPHMAP2_ALIGN": {
"graphmap2": "0.6.3"
}
}
],
"timestamp": "2026-05-11T21:53:33.81849412",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-14T11:52:49.613989705"
"nf-test": "0.9.5",
"nextflow": "26.03.2"
}
},
"sarscov2 - fastq - fasta - index": {
"content": [
[
"versions.yml:md5,0c397959d073e21ab58ceed89978f8bb"
],
"test.sam"
{
"sam": [
[
{
"id": "test"
},
"test.sam"
]
],
"versions_graphmap2": [
[
"GRAPHMAP2_ALIGN",
"graphmap2",
"0.6.3"
]
]
}
],
"timestamp": "2026-05-11T21:53:19.638775357",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-14T11:52:41.96001224"
"nf-test": "0.9.5",
"nextflow": "26.03.2"
}
}
}
20 changes: 5 additions & 15 deletions modules/nf-core/graphmap2/index/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,8 @@ process GRAPHMAP2_INDEX {
path fasta

output:
path "*.gmidx" , emit: index
path "versions.yml" , emit: versions
path "*.gmidx", emit: index
tuple val("${task.process}"), val('graphmap2'), eval("graphmap2 2>&1 | sed -n 's/Version: v//p'"), emit: versions_graphmap2, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -21,25 +21,15 @@ process GRAPHMAP2_INDEX {
"""
graphmap2 \\
align \\
-t $task.cpus \\
-t ${task.cpus} \\
-I \\
$args \\
-r $fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
graphmap2: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
END_VERSIONS
${args} \\
-r ${fasta}
"""

stub:

"""
touch ${fasta}.gmidx

cat <<-END_VERSIONS > versions.yml
"${task.process}":
graphmap2: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
END_VERSIONS
"""
}
32 changes: 24 additions & 8 deletions modules/nf-core/graphmap2/index/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
name: graphmap2_index
description: A versatile pairwise aligner for genomic and spliced nucleotide sequences
description: A versatile pairwise aligner for genomic and spliced nucleotide
sequences
keywords:
- index
- fasta
Expand All @@ -10,7 +11,8 @@ tools:
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
homepage: https://github.com/lbcb-sci/graphmap2
documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads
licence: ["MIT"]
licence:
- "MIT"
identifier: biotools:Graphmap2
input:
- fasta:
Expand All @@ -25,13 +27,27 @@ output:
description: Index file in gmidx format
pattern: "*.gmidx"
ontologies: []
versions_graphmap2:
- - ${task.process}:
type: string
description: The name of the process
- graphmap2:
type: string
description: The name of the tool
- "graphmap2 2>&1 | sed -n 's/Version: v//p'":
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
- graphmap2:
type: string
description: The name of the tool
- "graphmap2 2>&1 | sed -n 's/Version: v//p'":
type: eval
description: The expression to obtain the version of the tool
authors:
- "@yuukiiwa"
- "@drpatelh"
Expand Down
6 changes: 2 additions & 4 deletions modules/nf-core/graphmap2/index/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,15 +16,14 @@ nextflow_process {
process {
"""
input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)

"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand All @@ -36,15 +35,14 @@ nextflow_process {
process {
"""
input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)

"""
}
}

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