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feat: _idx -> _tbi (#1074)

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Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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Maxime U. Garcia 2021-11-15 17:49:20 +01:00 committed by GitHub
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commit 5b1ce484b9
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6 changed files with 27 additions and 27 deletions
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2
modules/gatk4/getpileupsummaries/main.nf
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@ -21,7 +21,7 @@ process GATK4_GETPILEUPSUMMARIES {
input: input:
tuple val(meta), path(bam), path(bai) tuple val(meta), path(bam), path(bai)
path variants path variants
path variants_idx path variants_tbi
path sites path sites
output: output:

2
modules/gatk4/getpileupsummaries/meta.yml
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@ -35,7 +35,7 @@ input:
type: file type: file
description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified. description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.
pattern: "*.vcf.gz" pattern: "*.vcf.gz"
- variants_idx: - variants_tbi:
type: file type: file
description: Index file for the germline resource. description: Index file for the germline resource.
pattern: "*.vcf.gz.tbi" pattern: "*.vcf.gz.tbi"

4
modules/gatk4/mutect2/main.nf
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@ -28,9 +28,9 @@ process GATK4_MUTECT2 {
path fastaidx path fastaidx
path dict path dict
path germline_resource path germline_resource
path germline_resource_idx path germline_resource_tbi
path panel_of_normals path panel_of_normals
path panel_of_normals_idx path panel_of_normals_tbi
output: output:
tuple val(meta), path("*.vcf.gz") , emit: vcf tuple val(meta), path("*.vcf.gz") , emit: vcf

8
modules/gatk4/mutect2/meta.yml
View file

@ -66,18 +66,18 @@ input:
type: file type: file
description: Population vcf of germline sequencing, containing allele fractions. description: Population vcf of germline sequencing, containing allele fractions.
pattern: "*.vcf.gz" pattern: "*.vcf.gz"
- germline_resource_idx: - germline_resource_tbi:
type: file type: file
description: Index file for the germline resource. description: Index file for the germline resource.
pattern: "*.vcf.gz_tbi" pattern: "*.vcf.gz.tbi"
- panel_of_normals: - panel_of_normals:
type: file type: file
description: vcf file to be used as a panel of normals. description: vcf file to be used as a panel of normals.
pattern: "*.vcf.gz" pattern: "*.vcf.gz"
- panel_of_normals_idx: - panel_of_normals_tbi:
type: file type: file
description: Index for the panel of normals. description: Index for the panel of normals.
pattern: "*.vcf.gz_tbi" pattern: "*.vcf.gz.tbi"
output: output:
- vcf: - vcf:

8
tests/modules/gatk4/getpileupsummaries/main.nf
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@ -11,10 +11,10 @@ workflow test_gatk4_getpileupsummaries_just_variants {
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ] file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ]
variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true) variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
variants_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true) variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
sites = [] sites = []
GATK4_GETPILEUPSUMMARIES ( input , variants , variants_idx , sites ) GATK4_GETPILEUPSUMMARIES ( input , variants , variants_tbi , sites )
} }
workflow test_gatk4_getpileupsummaries_separate_sites { workflow test_gatk4_getpileupsummaries_separate_sites {
@ -24,8 +24,8 @@ workflow test_gatk4_getpileupsummaries_separate_sites {
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ] file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ]
variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true) variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
variants_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true) variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
sites = file( "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.interval_list" , checkIfExists: true) sites = file( "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.interval_list" , checkIfExists: true)
GATK4_GETPILEUPSUMMARIES ( input , variants , variants_idx , sites ) GATK4_GETPILEUPSUMMARIES ( input , variants , variants_tbi , sites )
} }

30
tests/modules/gatk4/mutect2/main.nf
View file

@ -20,11 +20,11 @@ workflow test_gatk4_mutect2_tumor_normal_pair {
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true) germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
germline_resource_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true) germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true) panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
panel_of_normals_idx = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true) panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
GATK4_TEMPFIX_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx ) GATK4_TEMPFIX_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
} }
workflow test_gatk4_mutect2_tumor_single { workflow test_gatk4_mutect2_tumor_single {
@ -41,11 +41,11 @@ workflow test_gatk4_mutect2_tumor_single {
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true) germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
germline_resource_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true) germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true) panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
panel_of_normals_idx = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true) panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
GATK4_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx ) GATK4_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
} }
workflow test_gatk4_mutect2_cram_input { workflow test_gatk4_mutect2_cram_input {
@ -62,11 +62,11 @@ workflow test_gatk4_mutect2_cram_input {
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true) germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
germline_resource_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true) germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true) panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
panel_of_normals_idx = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true) panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
GATK4_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx ) GATK4_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
} }
workflow test_gatk4_mutect2_generate_pon { workflow test_gatk4_mutect2_generate_pon {
@ -83,11 +83,11 @@ workflow test_gatk4_mutect2_generate_pon {
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
germline_resource = [] germline_resource = []
germline_resource_idx = [] germline_resource_tbi = []
panel_of_normals = [] panel_of_normals = []
panel_of_normals_idx = [] panel_of_normals_tbi = []
GATK4_MUTECT2 ( input , run_single , run_pon, run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx ) GATK4_MUTECT2 ( input , run_single , run_pon, run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
} }
// mitochondria mode would ideally have some mitochondria test data, but since the mitochondria settings only increase detection sensitivity, we can use the chr22 data as a stand in as it is already a small dataset, the extra variants detected compared to generate_pon shows the mode is working. // mitochondria mode would ideally have some mitochondria test data, but since the mitochondria settings only increase detection sensitivity, we can use the chr22 data as a stand in as it is already a small dataset, the extra variants detected compared to generate_pon shows the mode is working.
@ -105,9 +105,9 @@ workflow test_gatk4_mutect2_mitochondria {
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
germline_resource = [] germline_resource = []
germline_resource_idx = [] germline_resource_tbi = []
panel_of_normals = [] panel_of_normals = []
panel_of_normals_idx = [] panel_of_normals_tbi = []
GATK4_MUTECT2 ( input , run_single , run_pon, run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx ) GATK4_MUTECT2 ( input , run_single , run_pon, run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
} }