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Whatshap/phase: add pedigree input #11128

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a79579d
Add new pedigree input
Apr 7, 2026
73e04d2
FIX: forgot to pass new input_ped
Apr 7, 2026
04f35fa
Use available pedigree file for testing
Apr 7, 2026
b159545
Merge branch 'master' into whatshap-phase-ped
tetedange13 Apr 7, 2026
71f7a54
FIX: whatshap/haplotag needs update too
Apr 7, 2026
0eebe47
Merge branch 'master' into whatshap-phase-ped
famosab Apr 8, 2026
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1 change: 1 addition & 0 deletions modules/nf-core/whatshap/haplotag/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/NA03697B2_new.pbmm2.repeats.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam.bai', checkIfExists: true),
[],
]

input[1] = Channel.of([
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4 changes: 3 additions & 1 deletion modules/nf-core/whatshap/phase/main.nf
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Expand Up @@ -8,7 +8,7 @@ process WHATSHAP_PHASE {
: 'community.wave.seqera.io/library/whatshap:2.8--7fe530bc624a3e5a' }"

input:
tuple val(meta), path(vcf), path(tbi), path(bam), path(bai)
tuple val(meta), path(vcf), path(tbi), path(bam), path(bai), path(pedigree)
tuple val(meta2), path(fasta), path(fai)

output:
Expand All @@ -22,6 +22,7 @@ process WHATSHAP_PHASE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def input_ped = pedigree ? "--ped ${pedigree}" : ""

if ("${vcf}" == "${prefix}.vcf" || "${vcf}" == "${prefix}.vcf.gz") {
error("Input and output names are the same, set prefix in module configuration to disambiguate!")
Expand All @@ -32,6 +33,7 @@ process WHATSHAP_PHASE {
--output ${prefix}.vcf \\
--reference ${fasta} \\
${args} \\
${input_ped} \\
${vcf} \\
${bam}

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4 changes: 4 additions & 0 deletions modules/nf-core/whatshap/phase/meta.yml
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Expand Up @@ -41,6 +41,10 @@ input:
type: file
description: BAM index file (optional but recommended)
pattern: "*.bai"
- pedigree:
type: file
description: Pedigree file (optional)
pattern: "*.ped"
- - meta2:
type: map
description: |
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2 changes: 2 additions & 0 deletions modules/nf-core/whatshap/phase/tests/main.nf.test
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Expand Up @@ -37,6 +37,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/NA03697B2_new.pbmm2.repeats.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam.bai', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM.ped', checkIfExists: true),
]

input[1] = Channel.of([
Expand Down Expand Up @@ -73,6 +74,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/NA03697B2_new.pbmm2.repeats.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam.bai', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM.ped', checkIfExists: true),
]

input[1] = Channel.of([
Expand Down
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