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Merge pull request #1711 from nvnieuwk/add-tbi-to-bcftools-concat

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Added optional input of index files to bcftools/concat
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nvnieuwk 2022-05-31 15:33:10 +02:00 committed by GitHub
commit 22a90dbd0f
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4 changed files with 33 additions and 7 deletions
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2
modules/bcftools/concat/main.nf
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@ -8,7 +8,7 @@ process BCFTOOLS_CONCAT {
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcfs)
tuple val(meta), path(vcfs), path(tbi)
output:
tuple val(meta), path("*.gz"), emit: vcf

5
modules/bcftools/concat/meta.yml
View file

@ -25,6 +25,11 @@ input:
description: |
List containing 2 or more vcf files
e.g. [ 'file1.vcf', 'file2.vcf' ]
- tbi:
type: files
description: |
List containing 2 or more index files (optional)
e.g. [ 'file1.tbi', 'file2.tbi' ]
output:
- meta:
type: map

18
tests/modules/bcftools/concat/main.nf
View file

@ -4,13 +4,25 @@ nextflow.enable.dsl = 2
include { BCFTOOLS_CONCAT } from '../../../../modules/bcftools/concat/main.nf'
workflow test_bcftools_concat {
workflow test_bcftools_concat_tbi {
input = [ [ id:'test3' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ]
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) ]
]
BCFTOOLS_CONCAT ( input )
}
workflow test_bcftools_concat_no_tbi {
input = [ [ id:'test3' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
[]
]
BCFTOOLS_CONCAT ( input )
}

15
tests/modules/bcftools/concat/test.yml
View file

@ -1,8 +1,17 @@
- name: bcftools concat test_bcftools_concat
command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
- name: bcftools concat test_bcftools_concat_tbi
command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
tags:
- bcftools/concat
- bcftools
- bcftools/concat
files:
- path: output/bcftools/test3.vcf.gz
md5sum: 35c88bfaad20101062e98beb217d7137
- name: bcftools concat test_bcftools_concat_no_tbi
command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
tags:
- bcftools
- bcftools/concat
files:
- path: output/bcftools/test3.vcf.gz
md5sum: 35c88bfaad20101062e98beb217d7137