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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>
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5 changed files with 34 additions and 8 deletions
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@ -11,7 +11,8 @@ process TABIX_TABIX {
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tuple val(meta), path(tab)
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output:
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tuple val(meta), path("*.tbi"), emit: tbi
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tuple val(meta), path("*.tbi"), optional:true, emit: tbi
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tuple val(meta), path("*.csi"), optional:true, emit: csi
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path "versions.yml" , emit: versions
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when:
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@ -31,6 +31,10 @@ output:
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type: file
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description: tabix index file
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pattern: "*.{tbi}"
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- csi:
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type: file
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description: coordinate sorted index file
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pattern: "*.{csi}"
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- versions:
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type: file
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description: File containing software versions
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@ -2,9 +2,10 @@
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nextflow.enable.dsl = 2
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include { TABIX_TABIX as TABIX_BED } from '../../../../modules/tabix/tabix/main.nf'
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include { TABIX_TABIX as TABIX_GFF } from '../../../../modules/tabix/tabix/main.nf'
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include { TABIX_TABIX as TABIX_VCF } from '../../../../modules/tabix/tabix/main.nf'
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include { TABIX_TABIX as TABIX_BED } from '../../../../modules/tabix/tabix/main.nf'
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include { TABIX_TABIX as TABIX_GFF } from '../../../../modules/tabix/tabix/main.nf'
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include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../modules/tabix/tabix/main.nf'
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include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../modules/tabix/tabix/main.nf'
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workflow test_tabix_tabix_bed {
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input = [ [ id:'B.bed' ], // meta map
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@ -22,10 +23,18 @@ workflow test_tabix_tabix_gff {
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TABIX_GFF ( input )
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}
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workflow test_tabix_tabix_vcf {
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workflow test_tabix_tabix_vcf_tbi {
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input = [ [ id:'test.vcf' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
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]
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TABIX_VCF ( input )
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TABIX_VCF_TBI ( input )
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}
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workflow test_tabix_tabix_vcf_csi {
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input = [ [ id:'test.vcf' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
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]
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TABIX_VCF_CSI ( input )
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}
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@ -10,8 +10,12 @@ process {
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ext.args = '-p gff'
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}
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withName: TABIX_VCF {
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withName: TABIX_VCF_TBI {
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ext.args = '-p vcf'
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}
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withName: TABIX_VCF_CSI {
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ext.args = '-p vcf --csi'
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}
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}
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@ -15,10 +15,18 @@
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- path: ./output/tabix/genome.gff3.gz.tbi
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md5sum: f79a67d95a98076e04fbe0455d825926
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- name: tabix tabix vcf
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command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
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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
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tags:
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- tabix
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- tabix/tabix
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files:
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- path: output/tabix/test.vcf.gz.tbi
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md5sum: 36e11bf96ed0af4a92caa91a68612d64
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- name: tabix tabix vcf csi
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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
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tags:
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- tabix
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- tabix/tabix
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files:
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- path: output/tabix/test.vcf.gz.csi
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md5sum: 5f930522d2b9dcdba2807b7da4dfa3fd
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