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new module: PERBASE #7457

Merged
merged 9 commits into from
Feb 18, 2025
Merged

new module: PERBASE #7457

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ef44c51
Add skeleton
camlloyd Feb 9, 2025
6987875
Update perbase
camlloyd Feb 10, 2025
b2b4b25
Update perbase
camlloyd Feb 10, 2025
ae3dc8d
Update perbase
camlloyd Feb 10, 2025
dab52a4
Harshil Alignment
camlloyd Feb 14, 2025
f6608c0
Merge branch 'master' into perbase
itrujnara Feb 15, 2025
ad12a35
Update perbase
camlloyd Feb 16, 2025
108ad36
Add ontology
camlloyd Feb 16, 2025
f656b93
Add ontology
camlloyd Feb 17, 2025
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7 changes: 7 additions & 0 deletions modules/nf-core/perbase/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda
dependencies:
- bioconda::perbase=0.10.2
49 changes: 49 additions & 0 deletions modules/nf-core/perbase/main.nf
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process PERBASE {
tag "$meta.id"
label 'process_low'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/perbase:0.10.2--h15397dd_0':
'biocontainers/perbase:0.10.2--h15397dd_0' }"

input:
tuple val(meta), path(bam), path(index)

output:
tuple val(meta), path("*.tsv.gz"), emit: tsv
path "versions.yml" , emit: versions

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

script:
def args = task.ext.args ?: ''
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Harshil alignment here would be great

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Should this be applied in the module template upstream?
https://github.com/nf-core/tools/blob/main/nf_core/module-template/main.nf

def prefix = task.ext.prefix ?: "${meta.id}"
"""
perbase \\
base-depth \\
$bam \\
$args \\
--threads $task.cpus \\
--bgzip \\
--output ${prefix}.tsv.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
perbase: \$(perbase --version |& sed '1!d ; s/perbase //')
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
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And here

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Should this be applied in the module template upstream?
https://github.com/nf-core/tools/blob/main/nf_core/module-template/main.nf

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Possibly, I need to discuss this with core

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Thanks, I can look at opening a PR if needed.

"""
echo "" | gzip > ${prefix}.tsv.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
perbase: \$(perbase --version |& sed '1!d ; s/perbase //')
END_VERSIONS
"""
}
63 changes: 63 additions & 0 deletions modules/nf-core/perbase/meta.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "perbase"
description: Per-base metrics on BAM/CRAM files.
keywords:
- bam
- cram
- depth
tools:
- "perbase":
description: "Per-base metrics on BAM/CRAM files."
homepage: "https://github.com/sstadick/perbase/blob/v0.10.2/README.md"
documentation: "https://github.com/sstadick/perbase/blob/v0.10.2/README.md"
tool_dev_url: "https://github.com/sstadick/perbase"
licence: ["MIT"]
identifier: biotools:perbase

input:
# Only when we have meta
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
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Please confirm that single_end is relevant here

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This is from the nf-core module template, but I believe it's still relevant here.

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Alright, thanks


- bam:
type: file
description: Sorted BAM/CRAM file
pattern: "*.{bam,cram}"
ontologies:
- edam: "http://edamontology.org/format_25722"
- edam: "http://edamontology.org/format_3462"

- index:
type: file
description: BAI/CRAI file
pattern: "*.{bai,crai}"
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Is there no suitable index format on EDAM?

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There is for BAI: https://edamontology.github.io/edam-browser/#format_3327
CRAI is still to be added: edamontology/edamontology#835
It looks like there are more general index entries too.

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Can you please add the best fit for each entry? It will make life easier for some people

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I have added the ontology for BAI.

The parent Data index format sounded the most appropriate, but has the notRecommendedForAnnotation attribute as it is a placeholder concept, rather than a specific file format.


output:
- tsv:
#Only when we have meta
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- "*.tsv.gz":
type: file
description: TSV file
pattern: "*.{tsv.gz}"
ontologies:
- edam: "http://edamontology.org/format_3475"

- versions:
- "versions.yml":
type: file
description: File containing software versions
pattern: "versions.yml"

authors:
- "@camlloyd"
maintainers:
- "@camlloyd"
113 changes: 113 additions & 0 deletions modules/nf-core/perbase/tests/main.nf.test
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nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "perbase"

test("homo_sapiens - illumina - cram") {


when {
process {
"""

input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true)
]
"""
}
}

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

}

test("homo_sapiens - illumina - cram - stub") {

options "-stub"

when {
process {
"""

input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true)
]
"""
}
}

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

}

test("homo_sapiens - illumina - bam") {


when {
process {
"""

input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
]
"""
}
}

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

}

test("homo_sapiens - illumina - bam - stub") {

options "-stub"

when {
process {
"""

input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
]
"""
}
}

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

}

}
142 changes: 142 additions & 0 deletions modules/nf-core/perbase/tests/main.nf.test.snap
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{
"homo_sapiens - illumina - bam - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [
"versions.yml:md5,b0d0beb66ff667db414fa86ee1e248dd"
],
"tsv": [
[
{
"id": "test",
"single_end": false
},
"test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,b0d0beb66ff667db414fa86ee1e248dd"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-02-10T09:15:57.123695003"
},
"homo_sapiens - illumina - bam": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.tsv.gz:md5,815a34cba6bd6aab7508212a03e6d467"
]
],
"1": [
"versions.yml:md5,b0d0beb66ff667db414fa86ee1e248dd"
],
"tsv": [
[
{
"id": "test",
"single_end": false
},
"test.tsv.gz:md5,815a34cba6bd6aab7508212a03e6d467"
]
],
"versions": [
"versions.yml:md5,b0d0beb66ff667db414fa86ee1e248dd"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-02-10T11:52:59.613861207"
},
"homo_sapiens - illumina - cram": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.tsv.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,b0d0beb66ff667db414fa86ee1e248dd"
],
"tsv": [
[
{
"id": "test",
"single_end": false
},
"test.tsv.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,b0d0beb66ff667db414fa86ee1e248dd"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-02-10T09:14:52.87095271"
},
"homo_sapiens - illumina - cram - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [
"versions.yml:md5,b0d0beb66ff667db414fa86ee1e248dd"
],
"tsv": [
[
{
"id": "test",
"single_end": false
},
"test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,b0d0beb66ff667db414fa86ee1e248dd"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-02-10T09:15:15.455581039"
}
}
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