8000 update vcfanno output by nvnieuwk · Pull Request #7353 · nf-core/modules · GitHub
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update vcfanno output #7353

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Merged
merged 5 commits into from
Jan 23, 2025
Merged

update vcfanno output #7353

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a402acd
update vcfanno output
nvnieuwk Jan 23, 2025
da7457f
update env.yaml
nvnieuwk Jan 23, 2025
dc8d53d
split output one another line
nvnieuwk Jan 23, 2025
d2bd8cc
fix linting
nvnieuwk Jan 23, 2025
d53e497
Merge branch 'master' into bgzip-vcfanno
nvnieuwk Jan 23, 2025
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2 changes: 2 additions & 0 deletions modules/nf-core/vcfanno/environment.yml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::htslib=1.21
- bioconda::vcfanno=0.3.5
22 changes: 14 additions & 8 deletions modules/nf-core/vcfanno/main.nf
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Expand Up @@ -4,8 +4,8 @@ process VCFANNO {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/vcfanno:0.3.5--h9ee0642_0':
'biocontainers/vcfanno:0.3.5--h9ee0642_0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d6/d6a1af15acc0fbec648812e07ccb4c1c39a926f3a98031a50f51c5b859e543e1/data':
'community.wave.seqera.io/library/htslib_vcfanno:398cde9953538855' }"

input:
tuple val(meta), path(vcf), path(tbi), path(specific_resources)
Expand All @@ -14,15 +14,18 @@ process VCFANNO {
path resources

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

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

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def lua_cmd = lua ? "--lua ${lua}" : ""
"""
vcfanno \\
Expand All @@ -31,7 +34,9 @@ process VCFANNO {
${lua_cmd} \\
${toml} \\
${vcf} \\
> ${prefix}.vcf
| bgzip ${args2} --threads ${task.cpus} \\
> ${prefix}.vcf.gz \\
&& tabix ${args3} ${prefix}.vcf.gz
8000

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -42,7 +47,8 @@ process VCFANNO {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf
touch ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
26 changes: 22 additions & 4 deletions modules/nf-core/vcfanno/meta.yml
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Expand Up @@ -53,10 +53,26 @@ output:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- "*.vcf":
type: file
description: Annotated VCF file
pattern: "*.vcf"
pattern: "*.vcf.gz"
- "*.vcf.gz":
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
pattern: "*.vcf.gz"
- tbi:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
pattern: "*.vcf.gz.tbi"
- "*.vcf.gz.tbi":
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
pattern: "*.vcf.gz.tbi"
- versions:
- versions.yml:
type: file
Expand All @@ -65,6 +81,8 @@ output:
authors:
- "@projectoriented"
- "@matthdsm"
- "@nvnieuwk"
maintainers:
- "@projectoriented"
- "@matthdsm"
- "@nvnieuwk"
64 changes: 56 additions & 8 deletions modules/nf-core/vcfanno/tests/main.nf.test.snap
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10000
Original file line number Diff line number Diff line change
@@ -1,12 +1,16 @@
{
"sarscov2 - [vcf(gz), tbi, vcf], [], toml, [vcf, tbi] - stub": {
"content": [
"test_compressed.vcf",
"test_compressed.vcf.gz",
[
"versions.yml:md5,5ff0991b612706ce15d82eb1564513b0"
]
],
"timestamp": "2023-12-06T12:18:25.69588598"
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-23T14:03:21.974046858"
},
"sarscov2 - [vcf(gz), tbi, vcf], [], toml, [vcf, tbi]": {
"content": [
Expand All @@ -17,27 +21,49 @@
"id": "test_compressed",
"single_end": false
},
"test_compressed.vcf:md5,d3cf5a6eaf6cca5b957833a313c5fbf4"
"test_compressed.vcf.gz:md5,d3cf5a6eaf6cca5b957833a313c5fbf4"
]
],
"1": [
[
{
"id": "test_compressed",
"single_end": false
},
"test_compressed.vcf.gz.tbi:md5,67a4272d5897fea5cc395dc87afc3629"
]
],
"2": [
"versions.yml:md5,5ff0991b612706ce15d82eb1564513b0"
],
"tbi": [
[
{
"id": "test_compressed",
"single_end": false
},
"test_compressed.vcf.gz.tbi:md5,67a4272d5897fea5cc395dc87afc3629"
]
],
"vcf": [
[
{
"id": "test_compressed",
"single_end": false
},
"test_compressed.vcf:md5,d3cf5a6eaf6cca5b957833a313c5fbf4"
"test_compressed.vcf.gz:md5,d3cf5a6eaf6cca5b957833a313c5fbf4"
]
],
"versions": [
"versions.yml:md5,5ff0991b612706ce15d82eb1564513b0"
]
}
],
"timestamp": "2023-12-06T12:21:13.209704154"
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-23T14:04:38.599392384"
},
"sarscov2 - [vcf, [], vcf], [], toml, [vcf, tbi]": {
"content": [
Expand All @@ -48,26 +74,48 @@
"id": "test_uncompressed",
"single_end": false
},
"test_uncompressed.vcf:md5,d3cf5a6eaf6cca5b957833a313c5fbf4"
"test_uncompressed.vcf.gz:md5,d3cf5a6eaf6cca5b957833a313c5fbf4"
]
],
"1": [
[
{
"id": "test_uncompressed",
"single_end": false
},
"test_uncompressed.vcf.gz.tbi:md5,67a4272d5897fea5cc395dc87afc3629"
]
],
"2": [
"versions.yml:md5,5ff0991b612706ce15d82eb1564513b0"
],
"tbi": [
[
{
"id": "test_uncompressed",
"single_end": false
},
"test_uncompressed.vcf.gz.tbi:md5,67a4272d5897fea5cc395dc87afc3629"
]
],
"vcf": [
[
{
"id": "test_uncompressed",
"single_end": false
},
"test_uncompressed.vcf:md5,d3cf5a6eaf6cca5b957833a313c5fbf4"
"test_uncompressed.vcf.gz:md5,d3cf5a6eaf6cca5b957833a313c5fbf4"
]
],
"versions": [
"versions.yml:md5,5ff0991b612706ce15d82eb1564513b0"
]
}
],
"timestamp": "2023-12-06T12:21:19.255212216"
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-23T14:04:48.104846161"
}
}
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