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Revert manta changes (#1518)

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* Fix typo

* Revert to have target bed matched with sample info

* Add comment on design decision
This commit is contained in:
FriederikeHanssen 2022-04-12 10:40:06 +02:00 committed by GitHub
parent 2d38566eca
commit ffedf09b6e
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2 changed files with 13 additions and 18 deletions
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5
modules/manta/germline/main.nf
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@ -8,11 +8,10 @@ process MANTA_GERMLINE {
'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input), path(index)
//Matching the target bed with the input sample allows to parallelize the same sample run across different intervals or a single bed file
tuple val(meta), path(input), path(index), path(target_bed), path(target_bed_tbi)
path fasta
path fasta_fai
tuple path(target_bed), path(target_bed_tbi)
output:
tuple val(meta), path("*candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf

26
tests/modules/manta/germline/main.nf
View file

@ -8,29 +8,27 @@ workflow test_manta_germline {
input = [
[ id:'test'], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)]
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)],
[],[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = [[],[]]
MANTA_GERMLINE ( input, fasta, fai, bed )
MANTA_GERMLINE ( input, fasta, fai )
}
workflow test_manta_germline_target_bed {
input = [
[ id:'test'], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = [
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)],
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
MANTA_GERMLINE ( input, fasta, fai, bed )
MANTA_GERMLINE ( input, fasta, fai )
}
workflow test_manta_germline_target_bed_jointcalling {
@ -39,14 +37,12 @@ workflow test_manta_germline_target_bed_jointcalling {
[file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true)],
[file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = [
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),],
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
MANTA_GERMLINE ( input, fasta, fai, bed )
MANTA_GERMLINE ( input, fasta, fai )
}