millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 19:18:17 +00:00
Code Issues Releases Packages Activity

Revert manta changes (#1518)

Browse source 
* 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
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
2 changed files with 13 additions and 18 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

5
modules/manta/germline/main.nf
View file

@ -8,11 +8,10 @@ process MANTA_GERMLINE {
'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }" 'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input: 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
path fasta_fai path fasta_fai
tuple path(target_bed), path(target_bed_tbi)
output: output:
tuple val(meta), path("*candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf 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 = [ input = [
[ id:'test'], // meta map [ 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'], 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) 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) 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 { workflow test_manta_germline_target_bed {
input = [ input = [
[ id:'test'], // meta map [ 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'], 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 = [
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], 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), 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 { 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']['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']['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']['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),],
]
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'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], 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 )
} }