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fix: merge bcftools/tabix and htslib/tabix tests into tabix/tabix
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4 changed files with 34 additions and 44 deletions
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@ -1,14 +0,0 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BCFTOOLS_TABIX } from '../../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
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workflow test_bcftools_tabix {
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def input = []
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input = [ [ id:'test' ], // meta map
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[ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) ] ]
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BCFTOOLS_TABIX ( input )
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}
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@ -1,8 +0,0 @@
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- name: bcftools tabix
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command: nextflow run ./tests/software/bcftools/tabix -entry test_bcftools_tabix -c tests/config/nextflow.config
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tags:
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- bcftools
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- bcftools_tabix
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files:
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- path: output/bcftools/test.vcf.gz.tbi
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md5sum: 06d52177f819730dd409157914534e8d
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@ -2,18 +2,30 @@
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nextflow.enable.dsl = 2
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include { HTSLIB_TABIX as TABIX_BED } from '../../../../software/htslib/tabix/main.nf' addParams( options: ['args': '-p bed'] )
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include { HTSLIB_TABIX as TABIX_GFF } from '../../../../software/htslib/tabix/main.nf' addParams( options: ['args': '-p gff'] )
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include { HTSLIB_TABIX as TABIX_VCF } from '../../../../software/htslib/tabix/main.nf' addParams( options: ['args': '-p vcf'] )
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include { TABIX_TABIX as TABIX_BED } from '../../../../software/tabix/tabix/main.nf' addParams( options: ['args': '-p bed'] )
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include { TABIX_TABIX as TABIX_GFF } from '../../../../software/tabix/tabix/main.nf' addParams( options: ['args': '-p gff'] )
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include { TABIX_TABIX as TABIX_VCF } from '../../../../software/tabix/tabix/main.nf' addParams( options: ['args': '-p vcf'] )
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workflow test_htslib_tabix_bed {
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TABIX_BED ( file("${launchDir}/tests/data/bed/B.bed.gz", checkIfExists: true) )
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workflow test_tabix_tabix_bed {
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def input = []
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input = [ [ id:'B.bed' ], // meta map
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[ file("${launchDir}/tests/data/bed/B.bed.gz", checkIfExists: true) ] ]
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TABIX_BED ( input )
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}
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workflow test_htslib_tabix_gff {
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TABIX_GFF ( file("${launchDir}/tests/data/gff/a.gff3.gz", checkIfExists: true) )
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workflow test_tabix_tabix_gff {
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def input = []
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input = [ [ id:'a.gff3' ], // meta map
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[ file("${launchDir}/tests/data/gff/a.gff3.gz", checkIfExists: true) ] ]
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TABIX_GFF ( input )
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}
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workflow test_htslib_tabix_vcf {
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TABIX_VCF ( file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) )
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workflow test_tabix_tabix_vcf {
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def input = []
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input = [ [ id:'test.vcf' ], // meta map
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[ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) ] ]
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TABIX_VCF ( input )
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}
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@ -1,26 +1,26 @@
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- name: htslib tabix bed
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command: nextflow run ./tests/software/htslib/tabix -entry test_htslib_tabix_bed -c tests/config/nextflow.config
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- name: tabix tabix bed
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command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_bed -c tests/config/nextflow.config
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tags:
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- htslib
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- htslib_tabix
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- tabix
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- tabix_tabix
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- bed
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files:
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- path: output/tabix/B.bed.gz.tbi
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md5sum: 6d657159c283200109f2ed082296f853
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- name: htslib tabix gff
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command: nextflow run ./tests/software/htslib/tabix -entry test_htslib_tabix_gff -c tests/config/nextflow.config
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- name: tabix tabix gff
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command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_gff -c tests/config/nextflow.config
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tags:
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- htslib
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- htslib_tabix
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- tabix
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- tabix_tabix
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- gff
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files:
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- path: output/tabix/a.gff3.gz.tbi
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md5sum: 77f666b63da45c6af8a394ab5642602e
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- name: htslib tabix vcf
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command: nextflow run ./tests/software/htslib/tabix -entry test_htslib_tabix_vcf -c tests/config/nextflow.config
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- name: tabix tabix vcf
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command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_vcf -c tests/config/nextflow.config
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tags:
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- htslib
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- htslib_tabix
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- tabix
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- tabix_tabix
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- vcf
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files:
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- path: output/tabix/test.vcf.gz.tbi
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