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feat: fastaidx -> fai (#1073)

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Maxime U. Garcia 2021-11-15 18:03:02 +01:00 committed by GitHub
parent 5b1ce484b9
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15 changed files with 47 additions and 42 deletions
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2
modules/gatk4/applybqsr/main.nf
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@ -21,7 +21,7 @@ process GATK4_APPLYBQSR {
input:
tuple val(meta), path(input), path(input_index), path(bqsr_table)
path fasta
path fastaidx
path fai
path dict
path intervals

5
modules/gatk4/applybqsr/meta.yml
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@ -34,12 +34,15 @@ input:
- fasta:
type: file
description: The reference fasta file
- fastaidx:
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- intervalsBed:
type: file
description: Bed file with the genomic regions included in the library (optional)

2
modules/gatk4/baserecalibrator/main.nf
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@ -21,7 +21,7 @@ process GATK4_BASERECALIBRATOR {
input:
tuple val(meta), path(input), path(input_index)
path fasta
path fastaidx
path fai
path dict
path intervalsBed
path knownSites

5
modules/gatk4/baserecalibrator/meta.yml
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@ -31,12 +31,15 @@ input:
- fasta:
type: file
description: The reference fasta file
- fastaidx:
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- intervalsBed:
type: file
description: Bed file with the genomic regions included in the library (optional)

2
modules/gatk4/createsomaticpanelofnormals/main.nf
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@ -21,7 +21,7 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
input:
tuple val(meta), path(genomicsdb)
path fasta
path fastaidx
path fai
path dict
output:

4
modules/gatk4/createsomaticpanelofnormals/meta.yml
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@ -28,10 +28,10 @@ input:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fastaidx:
- fai:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary

2
modules/gatk4/filtermutectcalls/main.nf
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@ -21,7 +21,7 @@ process GATK4_FILTERMUTECTCALLS {
input:
tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest)
path fasta
path fastaidx
path fai
path dict
output:

4
modules/gatk4/filtermutectcalls/meta.yml
View file

@ -53,10 +53,10 @@ input:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fastaidx:
- fai:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary

2
modules/gatk4/mutect2/main.nf
View file

@ -25,7 +25,7 @@ process GATK4_MUTECT2 {
val run_mito
val interval_label
path fasta
path fastaidx
path fai
path dict
path germline_resource
path germline_resource_tbi

4
modules/gatk4/mutect2/meta.yml
View file

@ -54,10 +54,10 @@ input:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fastaidx:
- fai:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary

6
subworkflows/nf-core/gatk_create_som_pon/main.nf
View file

@ -14,7 +14,7 @@ workflow GATK_CREATE_SOM_PON {
take:
ch_mutect2_in // channel: [ val(meta), [ input ], [ input_index ], [] ]
fasta // channel: /path/to/reference/fasta
fastaidx // channel: /path/to/reference/fasta/index
fai // channel: /path/to/reference/fasta/index
dict // channel: /path/to/reference/fasta/dictionary
pon_name // channel: name for panel of normals
interval_file // channel: /path/to/interval/file
@ -25,7 +25,7 @@ workflow GATK_CREATE_SOM_PON {
//
//Perform variant calling for each sample using mutect2 module in panel of normals mode.
//
GATK4_MUTECT2 ( input , false , true, false , [] , fasta , fastaidx , dict , [], [] , [] , [] )
GATK4_MUTECT2 ( input, false, true, false, [], fasta, fai, dict, [], [], [], [] )
ch_versions = ch_versions.mix(GATK4_MUTECT2.out.versions.first())
//
@ -41,7 +41,7 @@ workflow GATK_CREATE_SOM_PON {
//Panel of normals made from genomicsdb workspace using createsomaticpanelofnormals.
//
GATK4_GENOMICSDBIMPORT.out.genomicsdb.view()
GATK4_CREATESOMATICPANELOFNORMALS ( GATK4_GENOMICSDBIMPORT.out.genomicsdb, fasta, fastaidx, dict )
GATK4_CREATESOMATICPANELOFNORMALS ( GATK4_GENOMICSDBIMPORT.out.genomicsdb, fasta, fai, dict )
ch_versions = ch_versions.mix(GATK4_CREATESOMATICPANELOFNORMALS.out.versions.first())
emit:

4
subworkflows/nf-core/gatk_create_som_pon/meta.yml
View file

@ -30,10 +30,10 @@ input:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fastaidx:
- fai:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary

18
tests/modules/gatk4/filtermutectcalls/main.nf
View file

@ -6,7 +6,7 @@ include { GATK4_FILTERMUTECTCALLS } from '../../../../modules/gatk4/filtermutect
workflow test_gatk4_filtermutectcalls_base {
input = [
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
@ -18,15 +18,15 @@ workflow test_gatk4_filtermutectcalls_base {
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
GATK4_FILTERMUTECTCALLS ( input, fasta, fastaidx, dict )
GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
}
workflow test_gatk4_filtermutectcalls_with_files {
input = [
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
@ -38,15 +38,15 @@ workflow test_gatk4_filtermutectcalls_with_files {
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
GATK4_FILTERMUTECTCALLS ( input, fasta, fastaidx, dict )
GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
}
workflow test_gatk4_filtermutectcalls_use_val {
input = [
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
@ -58,8 +58,8 @@ workflow test_gatk4_filtermutectcalls_use_val {
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
GATK4_FILTERMUTECTCALLS ( input, fasta, fastaidx, dict )
GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
}

24
tests/modules/gatk4/mutect2/main.nf
View file

@ -8,8 +8,8 @@ include { GATK4_MUTECT2 as GATK4_TEMPFIX_MUTECT2 } from '../../../../modules/gat
workflow test_gatk4_mutect2_tumor_normal_pair {
input = [ [ id:'test'], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) , file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) , file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
["testN"]
]
run_single = false
@ -17,14 +17,14 @@ workflow test_gatk4_mutect2_tumor_normal_pair {
run_mito = false
interval_label = []
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], 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_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_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_tbi , panel_of_normals , panel_of_normals_tbi )
GATK4_TEMPFIX_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
}
workflow test_gatk4_mutect2_tumor_single {
@ -38,14 +38,14 @@ workflow test_gatk4_mutect2_tumor_single {
run_mito = false
interval_label = []
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], 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_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_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_tbi , panel_of_normals , panel_of_normals_tbi )
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
}
workflow test_gatk4_mutect2_cram_input {
@ -59,14 +59,14 @@ workflow test_gatk4_mutect2_cram_input {
run_mito = false
interval_label = []
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], 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_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_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_tbi , panel_of_normals , panel_of_normals_tbi )
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
}
workflow test_gatk4_mutect2_generate_pon {
@ -80,14 +80,14 @@ workflow test_gatk4_mutect2_generate_pon {
run_mito = false
interval_label = []
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
germline_resource = []
germline_resource_tbi = []
panel_of_normals = []
panel_of_normals_tbi = []
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 )
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, 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.
@ -102,12 +102,12 @@ workflow test_gatk4_mutect2_mitochondria {
run_mito = true
interval_label = 'chr22'
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
germline_resource = []
germline_resource_tbi = []
panel_of_normals = []
panel_of_normals_tbi = []
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 )
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
}

5
tests/subworkflows/nf-core/gatk_create_som_pon/main.nf
View file

@ -16,11 +16,10 @@ workflow test_gatk_create_som_pon {
[] ]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
pon_name = "test_panel"
interval_file = file(params.test_data['homo_sapiens']['genome']['genome_interval_list'], checkIfExists: true)
GATK_CREATE_SOM_PON ( ch_mutect2_in, fasta, fastaidx, dict, pon_name, interval_file )
GATK_CREATE_SOM_PON ( ch_mutect2_in, fasta, fai, dict, pon_name, interval_file )
}