csi output in TABIX (#1579)

* Added: csi output to TABIX

* Added: tests for csi

* Fix tiddit/sv (#1580)

* Fix fasta ref option for TIDDIT_SV

* Add md5sum's to tiddit/sv tests

Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>

* Fix: prettier issues

Co-authored-by: Daniel Cooke <daniel.cooke@invitae.com>
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
This commit is contained in:
Praveen Raj S 2022-04-28 14:41:01 +02:00 committed by GitHub
parent cdefbec669
commit b3e9b88e80
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
5 changed files with 34 additions and 8 deletions

View file

@ -11,7 +11,8 @@ process TABIX_TABIX {
tuple val(meta), path(tab)
output:
tuple val(meta), path("*.tbi"), emit: tbi
tuple val(meta), path("*.tbi"), optional:true, emit: tbi
tuple val(meta), path("*.csi"), optional:true, emit: csi
path "versions.yml" , emit: versions
when:

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@ -31,6 +31,10 @@ output:
type: file
description: tabix index file
pattern: "*.{tbi}"
- csi:
type: file
description: coordinate sorted index file
pattern: "*.{csi}"
- versions:
type: file
description: File containing software versions

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@ -2,9 +2,10 @@
nextflow.enable.dsl = 2
include { TABIX_TABIX as TABIX_BED } from '../../../../modules/tabix/tabix/main.nf'
include { TABIX_TABIX as TABIX_GFF } from '../../../../modules/tabix/tabix/main.nf'
include { TABIX_TABIX as TABIX_VCF } from '../../../../modules/tabix/tabix/main.nf'
include { TABIX_TABIX as TABIX_BED } from '../../../../modules/tabix/tabix/main.nf'
include { TABIX_TABIX as TABIX_GFF } from '../../../../modules/tabix/tabix/main.nf'
include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../modules/tabix/tabix/main.nf'
include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../modules/tabix/tabix/main.nf'
workflow test_tabix_tabix_bed {
input = [ [ id:'B.bed' ], // meta map
@ -22,10 +23,18 @@ workflow test_tabix_tabix_gff {
TABIX_GFF ( input )
}
workflow test_tabix_tabix_vcf {
workflow test_tabix_tabix_vcf_tbi {
input = [ [ id:'test.vcf' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
]
TABIX_VCF ( input )
TABIX_VCF_TBI ( input )
}
workflow test_tabix_tabix_vcf_csi {
input = [ [ id:'test.vcf' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
]
TABIX_VCF_CSI ( input )
}

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@ -10,8 +10,12 @@ process {
ext.args = '-p gff'
}
withName: TABIX_VCF {
withName: TABIX_VCF_TBI {
ext.args = '-p vcf'
}
withName: TABIX_VCF_CSI {
ext.args = '-p vcf --csi'
}
}

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@ -15,10 +15,18 @@
- path: ./output/tabix/genome.gff3.gz.tbi
md5sum: f79a67d95a98076e04fbe0455d825926
- name: tabix tabix vcf
command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf_tbi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
tags:
- tabix
- tabix/tabix
files:
- path: output/tabix/test.vcf.gz.tbi
md5sum: 36e11bf96ed0af4a92caa91a68612d64
- name: tabix tabix vcf csi
command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf_csi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
tags:
- tabix
- tabix/tabix
files:
- path: output/tabix/test.vcf.gz.csi
md5sum: 5f930522d2b9dcdba2807b7da4dfa3fd