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Sentieon/Haplotyper: Recal table is sample specific #6078

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Aug 1, 2024
Merged

Sentieon/Haplotyper: Recal table is sample specific #6078

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7bedd59
recal table is sample specific
FriederikeHanssen Aug 1, 2024
00f0ca3
Merge branch 'master' into fix_haplotyper
FriederikeHanssen Aug 1, 2024
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3 changes: 1 addition & 2 deletions modules/nf-core/sentieon/haplotyper/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,11 @@ process SENTIEON_HAPLOTYPER {
'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"

input:
tuple val(meta), path(input), path(input_index), path(intervals)
tuple val(meta), path(input), path(input_index), path(intervals), path(recal_table)
tuple val(meta1), path(fasta)
tuple val(meta2), path(fai)
tuple val(meta3), path(dbsnp)
tuple val(meta4), path(dbsnp_tbi)
tuple val(meta5), path(recal_table)
val(emit_vcf)
val(emit_gvcf)

Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/sentieon/haplotyper/meta.yml
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Expand Up @@ -28,6 +28,9 @@ input:
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- recal_table:
type: file
description: Recalibration table from sentieon/qualcal (optional)
- fasta:
type: file
description: Genome fasta file
Expand All @@ -42,9 +45,6 @@ input:
- dbsnp_tbi:
type: file
description: VCF index of dbsnp (optional)
- recal_table:
type: file
description: Recalibration table from sentieon/qualcal (optional)
- emit_vcf:
type: string
description: |
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62 changes: 32 additions & 30 deletions modules/nf-core/sentieon/haplotyper/tests/main.nf.test
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Expand Up @@ -19,15 +19,15 @@ nextflow_process {
input[0] = [ [ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
[] // no intervals
[], // no intervals
[] // no recal table
]
input[1] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
input[2] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
input[3] = [[:],[]]
input[4] = [[:],[]]
input[5] = [[:],[]]
input[6] = 'variant'
input[7] = false
input[5] = 'variant'
input[6] = false
"""
}
}
Expand All @@ -54,15 +54,15 @@ nextflow_process {
input[0] = [ [ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
[] // no intervals
[], // no intervals
[] // no recal table
]
input[1] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
input[2] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
input[3] = [[:],[]]
input[4] = [[:],[]]
input[5] = [[:],[]]
input[6] = ''
input[7] = true
input[5] = ''
input[6] = true
"""
}
}
Expand All @@ -89,15 +89,15 @@ nextflow_process {
input[0] = [ [ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
[] // no intervals
[], // no intervals
[] // no recal table
]
input[1] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
input[2] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
input[3] = [[:],[]]
input[4] = [[:],[]]
input[5] = [[:],[]]
input[6] = 'variant'
input[7] = true
input[5] = 'variant'
input[6] = true
"""
}
}
Expand Down Expand Up @@ -126,15 +126,15 @@ nextflow_process {
input[0] = [ [ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
[]
]
input[1] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
input[2] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
input[3] = [[:],[]]
input[4] = [[:],[]]
input[5] = [[:],[]]
input[6] = 'variant'
input[7] = true
input[5] = 'variant'
input[6] = true
"""
}
}
Expand Down Expand Up @@ -163,15 +163,15 @@ nextflow_process {
input[0] = [ [ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
[]
]
input[1] = [[id: 'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
input[2] = [[id: 'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
input[3] = [[id: 'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true)]
input[4] = [[id: 'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true)]
input[5] = [[:],[]]
input[6] = 'variant'
input[7] = true
input[5] = 'variant'
input[6] = true
"""
}
}
Expand Down Expand Up @@ -218,18 +218,20 @@ nextflow_process {
when {
process {
"""
input[0] = [ [ id:'test' ], // meta map
recal_table = SENTIEON_QUALCAL.out.table
bam = Channel.of([ [ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
[] // no intervals
]
[] // no intervals

])
input[0] = bam.join(recal_table)
input[1] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
input[2] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
input[3] = [[:],[]]
input[4] = [[:],[]]
input[5] = SENTIEON_QUALCAL.out.table
input[6] = 'variant'
input[7] = false
input[5] = 'variant'
input[6] = false
"""
}
}
Expand Down Expand Up @@ -257,15 +259,15 @@ nextflow_process {
input[0] = [ [ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
[] // no intervals
[], // no intervals
[] // no recal table
]
input[1] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
input[2] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
input[3] = [[:],[]]
input[4] = [[:],[]]
input[5] = [[:],[]]
input[6] = 'variant'
input[7] = true
input[5] = 'variant'
input[6] = true
"""
}
}
Expand Down
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