mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
Update version for log4j vulnerability (#1176)
* Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
This commit is contained in:
FriederikeHanssen
GitHub
parent
02218ab5a0
commit
50eafb19c6
43 changed files with 253 additions and 211 deletions
|
|
@ -2,10 +2,10 @@ process GATK4_APPLYBQSR {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(bqsr_table)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_APPLYVQSR {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bed)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_CALCULATECONTAMINATION {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(pileup), path(matched)
|
||||
|
|
@ -13,7 +13,7 @@ process GATK4_CALCULATECONTAMINATION {
|
|||
|
||||
output:
|
||||
tuple val(meta), path('*.contamination.table'), emit: contamination
|
||||
tuple val(meta), path('*.segmentation.table') , optional:true, emit: segmentation
|
||||
tuple val(meta), path('*.segmentation.table') , emit: segmentation, optional:true
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY {
|
|||
tag "$fasta"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
path fasta
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(genomicsdb)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(cram)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_1':
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_1' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(recal_table)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(intervalfile), val(intervalval), path(wspace)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(gvcf), path(gvcf_index)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.0.0--0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(feature_file)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(interval_list)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(f1r2)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bams)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(aligned)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEVCFS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcfs)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MUTECT2 {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta) , path(input) , path(input_index) , val(which_norm)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_REVERTSAM {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(vcf_tbi)
|
||||
|
|
|
|||
|
|
@ -118,6 +118,7 @@ params {
|
|||
genome_21_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
|
||||
genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
|
||||
genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
|
||||
genome_21_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list"
|
||||
|
||||
dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
|
||||
dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
|
||||
|
|
@ -125,6 +126,9 @@ params {
|
|||
gnomad_r2_1_1_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi"
|
||||
mills_and_1000g_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
|
||||
mills_and_1000g_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
|
||||
syntheticvcf_short_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
|
||||
syntheticvcf_short_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
|
||||
|
||||
hapmap_3_3_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz"
|
||||
hapmap_3_3_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi"
|
||||
res_1000g_omni2_5_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz"
|
||||
|
|
@ -133,9 +137,10 @@ params {
|
|||
res_1000g_phase1_snps_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi"
|
||||
dbsnp_138_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz"
|
||||
dbsnp_138_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi"
|
||||
|
||||
syntheticvcf_short_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
|
||||
syntheticvcf_short_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
|
||||
gnomad_r2_1_1_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz"
|
||||
gnomad_r2_1_1_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi"
|
||||
mills_and_1000g_indels_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz"
|
||||
mills_and_1000g_indels_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi"
|
||||
|
||||
index_salmon = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon"
|
||||
repeat_expansions = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
|
||||
|
|
@ -175,6 +180,10 @@ params {
|
|||
test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
|
||||
test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
|
||||
|
||||
|
||||
mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
|
||||
mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
|
||||
|
||||
test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
|
||||
test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
|
||||
test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
|
||||
|
|
|
|||
|
|
@ -1,26 +1,32 @@
|
|||
- name: gatk4 applybqsr test_gatk4_applybqsr
|
||||
command: nextflow run ./tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
|
||||
tags:
|
||||
- gatk4/applybqsr
|
||||
- gatk4
|
||||
- gatk4/applybqsr
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: af56f5dd81b95070079d54670507f530
|
||||
md5sum: 8fe7c4b5fcfb72d24ed8102eb26e42fb
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 8a2fb7c7e38f24d3fefd5e84da701b00
|
||||
|
||||
- name: gatk4 applybqsr test_gatk4_applybqsr_intervals
|
||||
command: nextflow run ./tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
|
||||
tags:
|
||||
- gatk4/applybqsr
|
||||
- gatk4
|
||||
- gatk4/applybqsr
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 0cbfa4be143e988d56ce741b5077510e
|
||||
md5sum: a7a1d1373ac1529abbc5e05359718ab1
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 550eecbb88887fadf8c62c5992ae48af
|
||||
|
||||
- name: gatk4 applybqsr test_gatk4_applybqsr_cram
|
||||
command: nextflow run ./tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
|
||||
tags:
|
||||
- gatk4/applybqsr
|
||||
- gatk4
|
||||
- gatk4/applybqsr
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 720ef7453fc3c9def18bbe396062346c
|
||||
md5sum: a333f80284a89a8daab28d3686a0b365
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 57933f27b3a31b05af3f7c248d365396
|
||||
|
|
|
|||
|
|
@ -1,17 +1,21 @@
|
|||
- name: gatk4 applyvqsr test_gatk4_applyvqsr
|
||||
command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/applyvqsr
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 984c932ee9a5683b18e22a369aa5c9e7
|
||||
|
||||
- name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific
|
||||
command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr_allele_specific -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/applyvqsr
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 3b55f26c94c5f145f10ef4c5f83ec3cc
|
||||
|
|
|
|||
|
|
@ -1,28 +1,34 @@
|
|||
- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_tumor_only
|
||||
command: nextflow run ./tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_tumor_only -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_tumor_only -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
|
||||
tags:
|
||||
- gatk4/calculatecontamination
|
||||
- gatk4
|
||||
- gatk4/calculatecontamination
|
||||
files:
|
||||
- path: output/gatk4/test.contamination.table
|
||||
md5sum: 5fdcf1728cf98985ce31c038eb24e05c
|
||||
md5sum: 46c708c943b453da89a3da08acfdb2a7
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 6f2396e71389cdfd184f91222c24fe8d
|
||||
|
||||
- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair
|
||||
command: nextflow run ./tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
|
||||
tags:
|
||||
- gatk4/calculatecontamination
|
||||
- gatk4
|
||||
- gatk4/calculatecontamination
|
||||
files:
|
||||
- path: output/gatk4/test.contamination.table
|
||||
md5sum: 5fdcf1728cf98985ce31c038eb24e05c
|
||||
md5sum: 46c708c943b453da89a3da08acfdb2a7
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 26863fa1e7e7d50d1a10761eced26062
|
||||
|
||||
- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation
|
||||
command: nextflow run ./tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
|
||||
tags:
|
||||
- gatk4/calculatecontamination
|
||||
- gatk4
|
||||
- gatk4/calculatecontamination
|
||||
files:
|
||||
- path: output/gatk4/test.contamination.table
|
||||
md5sum: 5fdcf1728cf98985ce31c038eb24e05c
|
||||
md5sum: 46c708c943b453da89a3da08acfdb2a7
|
||||
- path: output/gatk4/test.segmentation.table
|
||||
md5sum: 91f28bfe4727a3256810927fc5eba92f
|
||||
md5sum: f4643d9319bde4efbfbe516d6fb13052
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 8b1191953ff20660e06e2a5d79e96b02
|
||||
|
|
|
|||
|
|
@ -1,17 +1,19 @@
|
|||
- name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end
|
||||
command: nextflow run ./tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/fastqtosam/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config -c ./tests/modules/gatk4/fastqtosam/nextflow.config
|
||||
tags:
|
||||
- gatk4/fastqtosam
|
||||
- gatk4
|
||||
- gatk4/fastqtosam
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 0a0d308b219837977b8df9daa26db7de
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: db3fa4b463427b08e32a5d8264be59c1
|
||||
|
||||
- name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end
|
||||
command: nextflow run ./tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/fastqtosam/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config -c ./tests/modules/gatk4/fastqtosam/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/fastqtosam
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 0a0d308b219837977b8df9daa26db7de
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: f4e35e46a29d8faebda5e852f9d0a132
|
||||
|
|
|
|||
|
|
@ -17,9 +17,9 @@ workflow test_gatk4_filtermutectcalls_base {
|
|||
[]
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
|
||||
}
|
||||
|
|
@ -37,9 +37,9 @@ workflow test_gatk4_filtermutectcalls_with_files {
|
|||
[]
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
|
||||
}
|
||||
|
|
@ -57,9 +57,9 @@ workflow test_gatk4_filtermutectcalls_use_val {
|
|||
'20.0'
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -6,9 +6,8 @@
|
|||
files:
|
||||
- path: output/gatk4/test.filtered.vcf.gz
|
||||
- path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
|
||||
md5sum: 98e1b87a52999eb8f429ef4a7877eb3f
|
||||
md5sum: 55f228e5520c8b9fbac017d3a3a6c5fd
|
||||
- path: output/gatk4/test.filtered.vcf.gz.tbi
|
||||
md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4
|
||||
|
||||
- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_with_files
|
||||
command: nextflow run ./tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_with_files -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtermutectcalls/nextflow.config
|
||||
|
|
@ -18,9 +17,8 @@
|
|||
files:
|
||||
- path: output/gatk4/test.filtered.vcf.gz
|
||||
- path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
|
||||
md5sum: 98e1b87a52999eb8f429ef4a7877eb3f
|
||||
md5sum: 9ae27fbd04af1a2ea574e2ff1c3a683b
|
||||
- path: output/gatk4/test.filtered.vcf.gz.tbi
|
||||
md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4
|
||||
|
||||
- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_use_val
|
||||
command: nextflow run ./tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_use_val -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtermutectcalls/nextflow.config
|
||||
|
|
@ -30,6 +28,5 @@
|
|||
files:
|
||||
- path: output/gatk4/test.filtered.vcf.gz
|
||||
- path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
|
||||
md5sum: 98e1b87a52999eb8f429ef4a7877eb3f
|
||||
md5sum: 95cc3e37705bd3b97a292c5d46ab82f3
|
||||
- path: output/gatk4/test.filtered.vcf.gz.tbi
|
||||
md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
- path: output/gatk4/test.table
|
||||
md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 50238fd0f3b6f4efb2b5335b6324f905
|
||||
md5sum: 2fa1214574359aa7c4e2212efbae3714
|
||||
|
||||
- name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple
|
||||
command: nextflow run tests/modules/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c tests/config/nextflow.config
|
||||
|
|
@ -18,4 +18,4 @@
|
|||
- path: output/gatk4/test.table
|
||||
md5sum: 0c1257eececf95db8ca378272d0f21f9
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: c6ce163062dd3609848fc5bc10660427
|
||||
md5sum: 92c17a728cef6d458491bcec6dac3e0c
|
||||
|
|
|
|||
|
|
@ -1,8 +1,8 @@
|
|||
- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_create_genomicsdb
|
||||
command: nextflow run ./tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_create_genomicsdb -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_create_genomicsdb -c tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
|
||||
tags:
|
||||
- gatk4/genomicsdbimport
|
||||
- gatk4
|
||||
- gatk4/genomicsdbimport
|
||||
files:
|
||||
- path: output/gatk4/test/__tiledb_workspace.tdb
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
|
|
@ -18,21 +18,27 @@
|
|||
- "FORMAT=<ID=AD,Number=R,Type=Integer,Description="
|
||||
- path: output/gatk4/test/vidmap.json
|
||||
md5sum: 18d3f68bd2cb6f4474990507ff95017a
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 92e9e7db68d22df72adc02e59fab1eb7
|
||||
|
||||
- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_get_intervalslist
|
||||
command: nextflow run ./tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_get_intervalslist -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_get_intervalslist -c tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
|
||||
tags:
|
||||
- gatk4/genomicsdbimport
|
||||
- gatk4
|
||||
- gatk4/genomicsdbimport
|
||||
files:
|
||||
- path: output/gatk4/test.interval_list
|
||||
md5sum: 4c85812ac15fc1cd29711a851d23c0bf
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: b3fcd07c2f498a2ad503912524d74294
|
||||
- path: output/untar/versions.yml
|
||||
md5sum: 8f080677b109aea2cfca50208b077534
|
||||
|
||||
- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_update_genomicsdb
|
||||
command: nextflow run ./tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_update_genomicsdb -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_update_genomicsdb -c tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
|
||||
tags:
|
||||
- gatk4/genomicsdbimport
|
||||
- gatk4
|
||||
- gatk4/genomicsdbimport
|
||||
files:
|
||||
- path: output/gatk4/test_genomicsdb/__tiledb_workspace.tdb
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
|
|
@ -41,10 +47,14 @@
|
|||
- path: output/gatk4/test_genomicsdb/chr22$1$40001/.__consolidation_lock
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
- path: output/gatk4/test_genomicsdb/chr22$1$40001/__array_schema.tdb
|
||||
md5sum: 35e7fdd18149be80c0c3f56fa1f23971
|
||||
md5sum: 6709e67921ae840bf61fbfb192554eda
|
||||
- path: output/gatk4/test_genomicsdb/chr22$1$40001/genomicsdb_meta_dir/genomicsdb_column_bounds.json
|
||||
md5sum: 2502f79658bc000578ebcfddfc1194c0
|
||||
- path: output/gatk4/test_genomicsdb/vcfheader.vcf
|
||||
md5sum: 47a615385a49f9261e088104b903bb9b
|
||||
md5sum: 3717f34ad68ff491f40a138410b2667a
|
||||
- path: output/gatk4/test_genomicsdb/vidmap.json
|
||||
md5sum: 18d3f68bd2cb6f4474990507ff95017a
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: f204d259538a490b40c1fe787a3d6602
|
||||
- path: output/untar/versions.yml
|
||||
md5sum: 9b2916aea9790bdf427c0cb38109110c
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
- gatk4/genotypegvcfs
|
||||
files:
|
||||
- path: output/gatk4/test.genotyped.vcf.gz
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
- path: output/gatk4/test.genotyped.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input
|
||||
|
|
@ -15,7 +15,7 @@
|
|||
- gatk4/genotypegvcfs
|
||||
files:
|
||||
- path: output/gatk4/test.genotyped.vcf.gz
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
- path: output/gatk4/test.genotyped.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp
|
||||
|
|
@ -25,7 +25,7 @@
|
|||
- gatk4/genotypegvcfs
|
||||
files:
|
||||
- path: output/gatk4/test.genotyped.vcf.gz
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
- path: output/gatk4/test.genotyped.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_intervals
|
||||
|
|
@ -35,7 +35,7 @@
|
|||
- gatk4/genotypegvcfs
|
||||
files:
|
||||
- path: output/gatk4/test.genotyped.vcf.gz
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
- path: output/gatk4/test.genotyped.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals
|
||||
|
|
@ -45,7 +45,7 @@
|
|||
- gatk4/genotypegvcfs
|
||||
files:
|
||||
- path: output/gatk4/test.genotyped.vcf.gz
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
contains: ['AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.05;SOR=0.693']
|
||||
- path: output/gatk4/test.genotyped.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input
|
||||
|
|
@ -55,7 +55,7 @@
|
|||
- gatk4/genotypegvcfs
|
||||
files:
|
||||
- path: output/gatk4/test.genotyped.vcf.gz
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
- path: output/gatk4/test.genotyped.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp
|
||||
|
|
@ -65,7 +65,7 @@
|
|||
- gatk4/genotypegvcfs
|
||||
files:
|
||||
- path: output/gatk4/test.genotyped.vcf.gz
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
- path: output/gatk4/test.genotyped.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_intervals
|
||||
|
|
@ -75,7 +75,7 @@
|
|||
- gatk4/genotypegvcfs
|
||||
files:
|
||||
- path: output/gatk4/test.genotyped.vcf.gz
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
- path: output/gatk4/test.genotyped.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals
|
||||
|
|
@ -85,5 +85,5 @@
|
|||
- gatk4/genotypegvcfs
|
||||
files:
|
||||
- path: output/gatk4/test.genotyped.vcf.gz
|
||||
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
|
||||
contains: ['AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.66;SOR=0.693']
|
||||
- path: output/gatk4/test.genotyped.vcf.gz.tbi
|
||||
|
|
|
|||
|
|
@ -10,8 +10,8 @@ workflow test_gatk4_getpileupsummaries_just_variants {
|
|||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], 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_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
|
||||
variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
|
||||
variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
sites = []
|
||||
|
||||
GATK4_GETPILEUPSUMMARIES ( input , variants , variants_tbi , sites )
|
||||
|
|
@ -23,9 +23,9 @@ workflow test_gatk4_getpileupsummaries_separate_sites {
|
|||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], 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_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)
|
||||
variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
|
||||
variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
sites = file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true)
|
||||
|
||||
GATK4_GETPILEUPSUMMARIES ( input , variants , variants_tbi , sites )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
- gatk4/getpileupsummaries
|
||||
files:
|
||||
- path: output/gatk4/test.pileups.table
|
||||
md5sum: 0d19674bef2ff0700d5b02b3463dd210
|
||||
md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
|
||||
|
||||
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites
|
||||
command: nextflow run ./tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/getpileupsummaries/nextflow.config
|
||||
|
|
@ -14,4 +14,4 @@
|
|||
- gatk4/getpileupsummaries
|
||||
files:
|
||||
- path: output/gatk4/test.pileups.table
|
||||
md5sum: 0d19674bef2ff0700d5b02b3463dd210
|
||||
md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
|
||||
|
|
|
|||
|
|
@ -1,8 +1,5 @@
|
|||
# We can't use an md5sum or check file contents because:
|
||||
# a) the path to the file is embedded inside it,
|
||||
# b) the file is binary so we can't check for text inside it.
|
||||
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed
|
||||
command: nextflow run ./tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/indexfeaturefile
|
||||
|
|
@ -10,30 +7,33 @@
|
|||
- path: output/gatk4/genome.bed.idx
|
||||
|
||||
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed_gz
|
||||
command: nextflow run ./tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed_gz -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed_gz -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/indexfeaturefile
|
||||
files:
|
||||
- path: output/gatk4/genome.bed.gz.tbi
|
||||
md5sum: 2eb6ed0a0b049efe4caa1413089dcd74
|
||||
md5sum: 4bc51e2351a6e83f20e13be75861f941
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: e574bd51e4c6d6ded5dcf3cd865dbf4a
|
||||
|
||||
# We can't use an md5sum or check file contents because:
|
||||
# a) the path to the file is embedded inside it,
|
||||
# b) the file is binary so we can't check for text inside it.
|
||||
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf
|
||||
command: nextflow run ./tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/indexfeaturefile
|
||||
files:
|
||||
- path: output/gatk4/test.genome.vcf.idx
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: fee70d33f4379ced035d8e851a3e08c6
|
||||
|
||||
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf_gz
|
||||
command: nextflow run ./tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/indexfeaturefile
|
||||
files:
|
||||
- path: output/gatk4/test.genome.vcf.gz.tbi
|
||||
md5sum: ea03cd1d1f178eefa656787537053c37
|
||||
md5sum: fedd68eaddf8d31257853d9da8325bd3
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 29bddb019f0fe04218cfc07f8203e022
|
||||
|
|
|
|||
|
|
@ -1,23 +1,27 @@
|
|||
- name: gatk4 markduplicates test_gatk4_markduplicates
|
||||
command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
|
||||
tags:
|
||||
- gatk4/markduplicates
|
||||
- gatk4
|
||||
- gatk4/markduplicates
|
||||
files:
|
||||
- path: output/gatk4/test.bai
|
||||
md5sum: e9c125e82553209933883b4fe2b8d7c2
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: f94271007c1ec8e56adfdd8e45a07bd0
|
||||
md5sum: 1c6b1372121eddccd086456aa1c174bf
|
||||
- path: output/gatk4/test.metrics
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 0e46677bdf1e5df892578cec6bc26dba
|
||||
|
||||
- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
|
||||
command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
|
||||
tags:
|
||||
- gatk4/markduplicates
|
||||
- gatk4
|
||||
- gatk4/markduplicates
|
||||
files:
|
||||
- path: output/gatk4/test.bai
|
||||
md5sum: bad71df9c876e72a5bc0a3e0fd755f92
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: e0462bd4fe2cf4beda71e1bd2c66235b
|
||||
md5sum: d1b85fb578a97f05b484c0d241a9aaad
|
||||
- path: output/gatk4/test.metrics
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 6844dc08e677455205e2270ac291c951
|
||||
|
|
|
|||
|
|
@ -3,28 +3,30 @@
|
|||
nextflow.enable.dsl = 2
|
||||
|
||||
include { GATK4_MUTECT2 } from '../../../../modules/gatk4/mutect2/main.nf'
|
||||
// used to run with the mitochondria mode setting as this increases sensitivity, allowing for some tumor_normal variants to be detected while the old test data is still in use, will be removed when new test data for sarek is available.
|
||||
include { GATK4_MUTECT2 as GATK4_TEMPFIX_MUTECT2 } from '../../../../modules/gatk4/mutect2/main.nf'
|
||||
|
||||
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)],
|
||||
["testN"]
|
||||
[ 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)
|
||||
],
|
||||
["normal"]
|
||||
]
|
||||
run_single = false
|
||||
run_pon = false
|
||||
run_mito = false
|
||||
interval_label = []
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
|
||||
germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
|
||||
panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
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 )
|
||||
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_tumor_single {
|
||||
|
|
@ -37,13 +39,13 @@ workflow test_gatk4_mutect2_tumor_single {
|
|||
run_pon = false
|
||||
run_mito = false
|
||||
interval_label = []
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
|
||||
germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
|
||||
panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
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 )
|
||||
}
|
||||
|
|
@ -58,13 +60,13 @@ workflow test_gatk4_mutect2_cram_input {
|
|||
run_pon = false
|
||||
run_mito = false
|
||||
interval_label = []
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
|
||||
germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
|
||||
panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
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 )
|
||||
}
|
||||
|
|
@ -79,9 +81,9 @@ workflow test_gatk4_mutect2_generate_pon {
|
|||
run_pon = true
|
||||
run_mito = false
|
||||
interval_label = []
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
germline_resource = []
|
||||
germline_resource_tbi = []
|
||||
panel_of_normals = []
|
||||
|
|
@ -93,8 +95,8 @@ workflow test_gatk4_mutect2_generate_pon {
|
|||
// 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.
|
||||
workflow test_gatk4_mutect2_mitochondria {
|
||||
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']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam'], checkIfExists: true)],
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam_bai'], checkIfExists: true)],
|
||||
[]
|
||||
]
|
||||
run_single = false
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
- path: output/gatk4/test.f1r2.tar.gz
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.stats
|
||||
md5sum: 887d54e393510f1d0aa2c33bc6155161
|
||||
md5sum: 17d2091015d04cbd4a26b7a67dc659e6
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single
|
||||
|
|
@ -18,7 +18,7 @@
|
|||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.stats
|
||||
md5sum: 106c5828b02b906c97922618b6072169
|
||||
md5sum: 55ed641e16089afb33cdbc478e202d3d
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 mutect2 test_gatk4_mutect2_cram_input
|
||||
|
|
@ -29,7 +29,7 @@
|
|||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.stats
|
||||
md5sum: 106c5828b02b906c97922618b6072169
|
||||
md5sum: 55ed641e16089afb33cdbc478e202d3d
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 mutect2 test_gatk4_mutect2_generate_pon
|
||||
|
|
@ -40,7 +40,7 @@
|
|||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.stats
|
||||
md5sum: 4f77301a125913170b8e9e7828b4ca3f
|
||||
md5sum: b569ce66bbffe9588b3d221e821023ee
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 mutect2 test_gatk4_mutect2_mitochondria
|
||||
|
|
|
|||
|
|
@ -1,8 +1,10 @@
|
|||
- name: gatk4 splitncigarreads test_gatk4_splitncigarreads
|
||||
command: nextflow run ./tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/splitncigarreads/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/splitncigarreads
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: bfe6d04a4072f97fdb97dbc502c9d3e2
|
||||
md5sum: 03068d510523c996814256d9811dc272
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: de130e0ab817304404f296b2e512b3b8
|
||||
|
|
|
|||
Loading…
Reference in a new issue