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modify test path - module gatk4 + added new module gatk4/haplotypecaller (#382)

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* new module: samtools/fastq

* solve conflict: pytest_software.yml

* solve linting conflicts

* solved EditorConfig linting problem

* Module samtools/fastq:
	* output compressed fastq.gz file(s)
	* add if conditionals for single/paired reads

* samtools/fastq: modified test.yml

* samtools/fastq: modified main.nf to avoid duplicated part of the script section

* fix README.md

* modify test path gatk4

* fix config

* Add new module gatk4/haplotypecaller

* solve check issues

* fix test.yml file

* fix test.yml gz.tbi

* Update software/gatk4/haplotypecaller/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/haplotypecaller/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/haplotypecaller/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/haplotypecaller/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/haplotypecaller/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/gatk4/haplotypecaller/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: suzannejin <suzanne.jin@crg.eu>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
suzannejin 2021-03-26 12:46:46 +01:00 committed by GitHub
parent e526eae472
commit 989fb7d5b7
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26 changed files with 319 additions and 109 deletions
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60
software/gatk4/haplotypecaller/functions.nf Normal file
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@ -0,0 +1,60 @@
/*
* -----------------------------------------------------
* Utility functions used in nf-core DSL2 module files
* -----------------------------------------------------
*/
/*
* Extract name of software tool from process name using $task.process
*/
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
/*
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
/*
* Tidy up and join elements of a list to return a path string
*/
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
/*
* Function to save/publish module results
*/
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_id) {
path_list.add(args.publish_id)
}
if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect()
ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename"
}
}
} else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename"
}
}
}

52
software/gatk4/haplotypecaller/main.nf Normal file
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@ -0,0 +1,52 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GATK4_HAPLOTYPECALLER {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
}
input:
tuple val(meta), path(bam), path(bai)
path fasta
path fai
path dict
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def avail_mem = 3
if (!task.memory) {
log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk \\
--java-options "-Xmx${avail_mem}g" \\
HaplotypeCaller \\
-R $fasta \\
-I $bam \\
-O ${prefix}.vcf.gz \\
$options.args
gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
"""
}

63
software/gatk4/haplotypecaller/meta.yml Normal file
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@ -0,0 +1,63 @@
name: gatk4_haplotypecaller
description: Call germline SNPs and indels via local re-assembly of haplotypes
keywords:
- gatk4
- haplotypecaller
- haplotype
tools:
- gatk4:
description: |
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file
pattern: "*.bam"
- bai:
type: file
description: Index of BAM file
pattern: "*.bam.bai"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- vcf:
type: file
description: Compressed VCF file
pattern: "*.vcf.gz"
- tbi:
type: file
description: Index of VCF file
pattern: "*.vcf.gz.tbi"
authors:
- "@suzannejin"

4
tests/config/pytest_software.yml
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@ -202,6 +202,10 @@ gatk4_fastqtosam:
- software/gatk4/fastqtosam/**
- tests/software/gatk4/fastqtosam/**
gatk4_haplotypecaller:
- software/gatk4/haplotypecaller/**
- tests/software/gatk4/haplotypecaller/**
gatk4_mergebamalignment:
- software/gatk4/mergebamalignment/**
- tests/software/gatk4/mergebamalignment/**

22
tests/software/gatk4/applybqsr/main.nf
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@ -6,25 +6,25 @@ include { GATK4_APPLYBQSR } from '../../../../software/gatk4/applybqsr/main.nf'
workflow test_gatk4_applybqsr {
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/gatk/test.table", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
dict = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.dict", checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_APPLYBQSR ( input, fasta, fai, dict, [] )
}
workflow test_gatk4_applybqsr_intervals {
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/gatk/test.table", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
dict = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.dict", checkIfExists: true)
intervals = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
intervals = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
GATK4_APPLYBQSR ( input, fasta, fai, dict, intervals )
}

12
tests/software/gatk4/applybqsr/test.yml
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@ -1,18 +1,18 @@
- name: gatk4 applybqsr test_gatk4_applybqsr
command: nextflow run tests/software/gatk4/applybqsr -entry test_gatk4_applybqsr -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_applybqsr
- gatk4
files:
- path: output/gatk4/test.bam
md5sum: 943a43de5f575a0435fe13072cbc15c8
md5sum: 139a5ffc7601ce3cfa7a896cd381542a
- name: "\e[3~"
- name: gatk4 applybqsr test_gatk4_applybqsr_intervals
command: nextflow run tests/software/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_applybqsr_intervals
- gatk4_applybqsr
- gatk4_applybqsr_intervals
- gatk4
files:
- path: output/gatk4/test.bam
md5sum: a92238a9a78da48bf437fd5b7d9790a3
md5sum: 5b1f6fa2525124c281f71e5a76d28482

42
tests/software/gatk4/baserecalibrator/main.nf
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@ -6,43 +6,43 @@ include { GATK4_BASERECALIBRATOR } from '../../../../software/gatk4/baserecalibr
workflow test_gatk4_baserecalibrator {
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
dict = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.dict", checkIfExists: true)
sites = file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true)
sites_tbi = file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi", checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, [], sites, sites_tbi )
}
workflow test_gatk4_baserecalibrator_intervals {
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
dict = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.dict", checkIfExists: true)
intervals = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
sites = file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true)
sites_tbi = file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi", checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
intervals = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, intervals, sites, sites_tbi )
}
workflow test_gatk4_baserecalibrator_multiple_sites {
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
dict = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.dict", checkIfExists: true)
sites = [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz", checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
sites = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)
]
sites_tbi = [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi", checkIfExists: true)
sites_tbi = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
]
GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, [], sites, sites_tbi )

8
tests/software/gatk4/baserecalibrator/test.yml
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@ -1,8 +1,8 @@
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator
command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_baserecalibrator
- gatk4
files:
- path: output/gatk4/test.table
md5sum: e2e43abdc0c943c1a54dae816d0b9ea7
@ -10,9 +10,9 @@
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_intervals
command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_intervals -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_baserecalibrator
- gatk4_baserecalibrator_intervals
- gatk4_baserecalibrator
- gatk4
files:
- path: output/gatk4/test.table
md5sum: 9ecb5f00a2229291705addc09c0ec231
@ -21,8 +21,8 @@
command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_multiple_sites -c tests/config/nextflow.config
tags:
- gatk4_baserecalibrator_multiple_sites
- gatk4
- gatk4_baserecalibrator
- gatk4
files:
- path: output/gatk4/test.table
md5sum: e2e43abdc0c943c1a54dae816d0b9ea7

4
tests/software/gatk4/bedtointervallist/main.nf
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@ -6,9 +6,9 @@ include { GATK4_BEDTOINTERVALLIST } from '../../../../software/gatk4/bedtointerv
workflow test_gatk4_bedtointervallist {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)]
[ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
]
dict = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.dict", checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_BEDTOINTERVALLIST ( input, dict )
}

4
tests/software/gatk4/bedtointervallist/test.yml
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@ -1,5 +1,5 @@
- name: gatk4 bedtointervallist
command: nextflow run ./tests/software/gatk4/bedtointervallist -entry test_gatk4_bedtointervallist -c tests/config/nextflow.config
- name: gatk4 bedtointervallist test_gatk4_bedtointervallist
command: nextflow run tests/software/gatk4/bedtointervallist -entry test_gatk4_bedtointervallist -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_bedtointervallist

2
tests/software/gatk4/createsequencedictionary/main.nf
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../../software/gatk4/createsequencedictionary/main.nf' addParams( options: [:] )
workflow test_gatk4_createsequencedictionary {
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
GATK4_CREATESEQUENCEDICTIONARY ( fasta )
}

8
tests/software/gatk4/createsequencedictionary/test.yml
View file

@ -1,8 +1,8 @@
- name: gatk4 createsequencedictionary
command: nextflow run ./tests/software/gatk4/createsequencedictionary -entry test_gatk4_createsequencedictionary -c tests/config/nextflow.config
- name: gatk4 createsequencedictionary test_gatk4_createsequencedictionary
command: nextflow run tests/software/gatk4/createsequencedictionary -entry test_gatk4_createsequencedictionary -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_createsequencedictionary
files:
- path: ./output/gatk4/test_genome.dict
md5sum: 829dd07bd0c9d3be2fd060238c0b37c3
- path: output/gatk4/genome.dict
md5sum: 7362679f176e0f52add03c08f457f646

6
tests/software/gatk4/fastqtosam/main.nf
View file

@ -6,7 +6,7 @@ include { GATK4_FASTQTOSAM } from '../../../../software/gatk4/fastqtosam/main.nf
workflow test_gatk4_fastqtosam_single_end {
input = [ [ id:'test', single_end:true ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
GATK4_FASTQTOSAM ( input )
@ -14,8 +14,8 @@ workflow test_gatk4_fastqtosam_single_end {
workflow test_gatk4_fastqtosam_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
]
GATK4_FASTQTOSAM ( input )

4
tests/software/gatk4/fastqtosam/test.yml
View file

@ -2,8 +2,8 @@
command: nextflow run tests/software/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config
tags:
- gatk4_fastqtosam_single_end
- gatk4_fastqtosam
- gatk4
- gatk4_fastqtosam
files:
- path: output/gatk4/test.bam
md5sum: 4967100b2e4912c0e4ce0976d946bafb
@ -12,8 +12,8 @@
command: nextflow run tests/software/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config
tags:
- gatk4_fastqtosam_paired_end
- gatk4_fastqtosam
- gatk4
- gatk4_fastqtosam
files:
- path: output/gatk4/test.bam
md5sum: 4967100b2e4912c0e4ce0976d946bafb

17
tests/software/gatk4/haplotypecaller/main.nf Normal file
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@ -0,0 +1,17 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GATK4_HAPLOTYPECALLER } from '../../../../software/gatk4/haplotypecaller/main.nf' addParams( options: [:] )
workflow test_gatk4_haplotypecaller {
input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict )
}

13
tests/software/gatk4/haplotypecaller/test.yml Normal file
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@ -0,0 +1,13 @@
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller
command: nextflow run tests/software/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller -c tests/config/nextflow.config
tags:
- gatk4_haplotypecaller
- gatk4
files:
- path: output/gatk4/test.vcf.gz
should_exist: true
contains:
- 'MT192765.1'
- '54.60'
- '37.32'
- path: output/gatk4/test.vcf.gz.tbi

8
tests/software/gatk4/mergebamalignment/main.nf
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@ -6,11 +6,11 @@ include { GATK4_MERGEBAMALIGNMENT } from '../../../../software/gatk4/mergebamali
workflow test_gatk4_mergebamalignment {
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_single_end.bam", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
]
unmapped = file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_unaligned.bam", checkIfExists: true)
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
dict = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.dict", checkIfExists: true)
unmapped = file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_MERGEBAMALIGNMENT ( input, unmapped, fasta, dict )
}

6
tests/software/gatk4/mergebamalignment/test.yml
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@ -1,8 +1,8 @@
- name: gatk4 mergebamalignment
command: nextflow run ./tests/software/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c tests/config/nextflow.config
- name: gatk4 mergebamalignment test_gatk4_mergebamalignment
command: nextflow run tests/software/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_mergebamalignment
files:
- path: output/gatk4/test.merged.bam
md5sum: 825816a6b288d644318c46cc9968e129
md5sum: bd4a5e2ea916826aadebb5878333e26f

14
tests/software/gatk4/mergevcfs/main.nf
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@ -6,10 +6,10 @@ include { GATK4_MERGEVCFS } from '../../../../software/gatk4/mergevcfs/main.nf'
workflow test_gatk4_mergevcfs {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test2.vcf", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
]
dict = file('tests/data/genomics/sarscov2/genome/genome.dict', checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_MERGEVCFS ( input, dict, false )
}
@ -17,10 +17,10 @@ workflow test_gatk4_mergevcfs {
workflow test_gatk4_mergevcfs_refdict {
def input = []
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test2.vcf", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
]
dict = file('tests/data/genomics/sarscov2/genome/genome.dict', checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_MERGEVCFS ( input, ref_dict, true )
GATK4_MERGEVCFS ( input, dict, true )
}

13
tests/software/gatk4/mergevcfs/test.yml
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@ -1,17 +1,18 @@
- name: gatk4 mergevcfs
command: nextflow run ./tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c tests/config/nextflow.config
- name: gatk4 mergevcfs test_gatk4_mergevcfs
command: nextflow run tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_mergevcfs
- gatk4
files:
- path: output/gatk4/test.merged.vcf.gz
md5sum: ff48f175e26db2d4b2957762f6d1c715
- name: gatk4 mergevcfs refdict
command: nextflow run ./tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config
- name: gatk4 mergevcfs test_gatk4_mergevcfs_refdict
command: nextflow run tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_mergevcfs
- gatk4
- gatk4_mergevcfs_refdict
files:
- path: output/gatk4/test.merged.vcf.gz
md5sum: ff48f175e26db2d4b2957762f6d1c715

2
tests/software/gatk4/revertsam/main.nf
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@ -6,7 +6,7 @@ include { GATK4_REVERTSAM } from '../../../../software/gatk4/revertsam/main.nf'
workflow test_gatk4_revertsam {
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.bam", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
GATK4_REVERTSAM ( input )

6
tests/software/gatk4/revertsam/test.yml
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@ -1,8 +1,8 @@
- name: gatk4 revertsam
command: nextflow run ./tests/software/gatk4/revertsam -entry test_gatk4_revertsam -c tests/config/nextflow.config
- name: gatk4 revertsam test_gatk4_revertsam
command: nextflow run tests/software/gatk4/revertsam -entry test_gatk4_revertsam -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_revertsam
files:
- path: output/gatk4/test.reverted.bam
md5sum: 6de199f7a0577e2a3fe7b3a9cb4ae25d
md5sum: f778310b18b83b49929eb648594f96dc

4
tests/software/gatk4/samtofastq/main.nf
View file

@ -6,7 +6,7 @@ include { GATK4_SAMTOFASTQ } from '../../../../software/gatk4/samtofastq/main.nf
workflow test_gatk4_samtofastq_single_end {
input = [ [ id:'test', single_end: true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_single_end.bam", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
]
GATK4_SAMTOFASTQ ( input )
@ -14,7 +14,7 @@ workflow test_gatk4_samtofastq_single_end {
workflow test_gatk4_samtofastq_paired_end {
input = [ [ id:'test', single_end: false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.bam", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
]
GATK4_SAMTOFASTQ ( input )

16
tests/software/gatk4/samtofastq/test.yml
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@ -1,21 +1,21 @@
- name: gatk4 samtofastq single-end
command: nextflow run ./tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c tests/config/nextflow.config
- name: gatk4 samtofastq test_gatk4_samtofastq_single_end
command: nextflow run tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_samtofastq
- gatk4_samtofastq_single_end
files:
- path: ./output/gatk4/test.fastq.gz
- path: output/gatk4/test.fastq.gz
md5sum: 50ace41d4c24467f24f8b929540a7797
- name: gatk4 samtofastq paired-end
command: nextflow run ./tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c tests/config/nextflow.config
- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end
command: nextflow run tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_samtofastq
- gatk4_samtofastq_paired_end
files:
- path: ./output/gatk4/test_2.fastq.gz
md5sum: 613bf64c023609e1c62ad6ce9e4be8d7
- path: ./output/gatk4/test_1.fastq.gz
- path: output/gatk4/test_1.fastq.gz
md5sum: cfea607c9d75fd9ea9704780ad3a499c
- path: output/gatk4/test_2.fastq.gz
md5sum: 613bf64c023609e1c62ad6ce9e4be8d7

8
tests/software/gatk4/splitncigarreads/main.nf
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@ -6,11 +6,11 @@ include { GATK4_SPLITNCIGARREADS } from '../../../../software/gatk4/splitncigarr
workflow test_gatk4_splitncigarreads {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.bam", checkIfExists: true)]
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
]
fasta = [ file("tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true),
file("tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true),
file("tests/data/genomics/sarscov2/genome/genome.dict", checkIfExists: true)
fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
]
GATK4_SPLITNCIGARREADS ( input, fasta )

6
tests/software/gatk4/splitncigarreads/test.yml
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@ -1,8 +1,8 @@
- name: gatk4 splitncigarreads
command: nextflow run ./tests/software/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config
- name: gatk4 splitncigarreads test_gatk4_splitncigarreads
command: nextflow run tests/software/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_splitncigarreads
files:
- path: output/gatk4/test.split_cigar.bam
md5sum: 9dd44d3988b9ff238a6b4771cdf13eba
md5sum: a8473bd4abc7b13751fc51b92531da4c