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Hiphase: update version to 1.5.0 and add phased bam file as an output #9477

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Hiphase: update version to 1.5.0 and add phased bam file as an output #9477

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8ed74a4
update hiphase verstion to 1.5.0
chaochaowong Nov 28, 2025
c8c15b4
add the *.phased.bam as an output file
chaochaowong Nov 28, 2025
3b64237
update test snapshot
chaochaowong Nov 28, 2025
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2 changes: 1 addition & 1 deletion modules/nf-core/hiphase/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::hiphase=1.4.5
- bioconda::hiphase=1.5.0
8 changes: 5 additions & 3 deletions modules/nf-core/hiphase/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,15 +4,16 @@ process HIPHASE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hiphase:1.4.5--h9ee0642_0':
'biocontainers/hiphase:1.4.5--h9ee0642_0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d4/d418cdbaff565e9c563c441c72d480f2605bb529712dd026068f1d0a7b246617/data':
'community.wave.seqera.io/library/hiphase:1.5.0--f36e5874e9287052' }"

input:
tuple val(meta), path(vcf), path(csi)
tuple val(meta) , path(vcf), path(csi)
tuple val(meta2), path(bam), path(bai)
tuple val(meta3), path(fasta)

output:
tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path("*.vcf"), emit: vcf
tuple val(meta), path("*.csv"), emit: csv
path "versions.yml" , emit: versions
Expand Down Expand Up @@ -44,6 +45,7 @@ process HIPHASE {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.phased.bam
touch ${prefix}.phased.vcf
touch ${prefix}.stats.csv
Expand Down
17 changes: 14 additions & 3 deletions modules/nf-core/hiphase/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,18 @@ input:
pattern: "*.{fasta}"
ontologies: []
output:
bam:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- "*.bam":
type: file
description: Phased BAM file with haplotag information
pattern: "*.bam"
ontologies:
- edam: http://edamontology.org/format_2572 # BAM
vcf:
- - meta:
type: map
Expand All @@ -66,7 +78,8 @@ output:
type: file
description: Phased VCF file
pattern: "*.vcf"
ontologies: []
ontologies:
- edam: http://edamontology.org/format_3016 # VCF
csv:
- - meta:
type: map
Expand All @@ -77,15 +90,13 @@ output:
type: file
description: stats associated with the phasing
pattern: "*.csv"

ontologies:
- edam: http://edamontology.org/format_3752 # CSV
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"

ontologies:
- edam: http://edamontology.org/format_3750 # YAML
authors:
Expand Down
62 changes: 47 additions & 15 deletions modules/nf-core/hiphase/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -7,19 +7,35 @@
{
"id": "test"
},
"test.phased.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.phased.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test"
},
"test.stats.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.phased.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
"versions.yml:md5,bdbe594b7912bdb1acefa03993d4ddf7"
[
{
"id": "test"
},
"test.stats.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [
"versions.yml:md5,d575d9f2bec6c1c5c4206b80ba7dfc96"
],
"bam": [
[
{
"id": "test"
},
"test.phased.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"csv": [
[
Expand All @@ -38,15 +54,15 @@
]
],
"versions": [
"versions.yml:md5,bdbe594b7912bdb1acefa03993d4ddf7"
"versions.yml:md5,d575d9f2bec6c1c5c4206b80ba7dfc96"
]
}
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "25.04.7"
},
"timestamp": "2024-10-25T15:30:16.272259201"
"timestamp": "2025-11-28T09:37:10.934639568"
},
"homo_sapiens pacbio [vcf] [csi] [bam] [bai] [fasta]": {
"content": [
Expand All @@ -56,19 +72,35 @@
{
"id": "test"
},
"test.phased.vcf:md5,8d27a1ef3c4b28662a7559ea2ccc4681"
"test.phased.bam:md5,ea563e2c998cabc656f3fead4161f6d8"
]
],
"1": [
[
{
"id": "test"
},
"test.stats.csv:md5,9901e909f6898db2b2a9d083a4f478d5"
"test.phased.vcf:md5,c4b24d778e57a1cc809de984c8bf9361"
]
],
"2": [
"versions.yml:md5,bdbe594b7912bdb1acefa03993d4ddf7"
[
{
"id": "test"
},
"test.stats.csv:md5,9901e909f6898db2b2a9d083a4f478d5"
]
],
"3": [
"versions.yml:md5,d575d9f2bec6c1c5c4206b80ba7dfc96"
],
"bam": [
[
{
"id": "test"
},
"test.phased.bam:md5,ea563e2c998cabc656f3fead4161f6d8"
]
],
"csv": [
[
Expand All @@ -83,18 +115,18 @@
{
"id": "test"
},
"test.phased.vcf:md5,8d27a1ef3c4b28662a7559ea2ccc4681"
"test.phased.vcf:md5,c4b24d778e57a1cc809de984c8bf9361"
]
],
"versions": [
"versions.yml:md5,bdbe594b7912bdb1acefa03993d4ddf7"
"versions.yml:md5,d575d9f2bec6c1c5c4206b80ba7dfc96"
]
}
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "25.04.7"
},
"timestamp": "2024-11-06T12:46:36.677573258"
"timestamp": "2025-11-28T09:37:04.541231653"
}
}
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