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Code Issues Releases Packages Activity

Manta consistancy (#1407)

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* update tests

* update

* update

* make the manta inputs consistant for germline/somatic/tumoronly

* match chromosomes to cram file (chr21)

* undo genotypegvfs

* undo genotypegvfs

* update manta input structure to match strelka. tuple(relevant input), path(fasta), path(fai)

* update tests

* fix typos

* fix typos

Co-authored-by: Smith Nicholas <smith@in.tum.de>
This commit is contained in:
nickhsmith 2022-03-18 13:30:03 +01:00 committed by GitHub
parent 7436eebf33
commit 979e57b7ac
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GPG key ID: 4AEE18F83AFDEB23
9 changed files with 74 additions and 67 deletions
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3
modules/manta/germline/main.nf
View file

@ -8,10 +8,9 @@ process MANTA_GERMLINE {
'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input), path(index)
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:

16
modules/manta/germline/meta.yml
View file

@ -31,14 +31,6 @@ input:
type: file
description: BAM/CRAM/SAM index file. For joint calling use a list of files.
pattern: "*.{bai,crai,sai}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fasta_fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
- target_bed:
type: file
description: BED file containing target regions for variant calling
@ -47,6 +39,14 @@ input:
type: file
description: Index for BED file containing target regions for variant calling
pattern: "*.{bed.tbi}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fasta_fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
output:
- meta:

4
modules/manta/somatic/main.nf
View file

@ -8,11 +8,9 @@ process MANTA_SOMATIC {
'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor)
tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi)
path fasta
path fai
path target_bed
path target_bed_tbi
output:
tuple val(meta), path("*.candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf

16
modules/manta/somatic/meta.yml
View file

@ -39,14 +39,6 @@ input:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
- target_bed:
type: file
description: BED file containing target regions for variant calling
@ -55,6 +47,14 @@ input:
type: file
description: Index for BED file containing target regions for variant calling
pattern: "*.{bed.tbi}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
output:
- meta:

4
modules/manta/tumoronly/main.nf
View file

@ -8,11 +8,9 @@ process MANTA_TUMORONLY {
'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input), path(input_index)
tuple val(meta), path(input), path(input_index), path(target_bed), path(target_bed_tbi)
path fasta
path fai
path target_bed
path target_bed_tbi
output:
tuple val(meta), path("*candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf

16
modules/manta/tumoronly/meta.yml
View file

@ -31,14 +31,6 @@ input:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
- target_bed:
type: file
description: BED file containing target regions for variant calling
@ -47,6 +39,14 @@ input:
type: file
description: Index for BED file containing target regions for variant calling
pattern: "*.{bed.tbi}"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
output:
- meta:

30
tests/modules/manta/germline/main.nf
View file

@ -7,30 +7,28 @@ include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
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'], 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)]
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']['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)
bed = [
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),
]
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),]
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)
bed = [
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),
]
MANTA_GERMLINE ( input, fasta, fai, bed )
MANTA_GERMLINE ( input, fasta, fai )
}

29
tests/modules/manta/somatic/main.nf
View file

@ -11,13 +11,30 @@ workflow test_manta_somatic {
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_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']['genome']['genome_bed_gz'], checkIfExists: true)
bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
MANTA_SOMATIC ( input, fasta, fai, bed, bed_tbi )
MANTA_SOMATIC ( input, fasta, fai )
}
workflow test_manta_somatic_target_bed {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true),
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
MANTA_SOMATIC ( input, fasta, fai )
}

23
tests/modules/manta/tumoronly/main.nf
View file

@ -8,28 +8,27 @@ workflow test_manta_tumoronly {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_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 = []
bed_tbi = []
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
MANTA_TUMORONLY ( input, fasta, fai, bed, bed_tbi )
MANTA_TUMORONLY ( input, fasta, fai )
}
workflow test_manta_tumoronly_target_bed {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_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)
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
MANTA_TUMORONLY ( input, fasta, fai, bed, bed_tbi )
MANTA_TUMORONLY ( input, fasta, fai )
}