feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059)

* feat: update gatk4 from 4.2.0.0 to 4.2.3.0

* update md5checksum

* commit all files

* actually checksum was good, but I suspect something fishy with the tests
This commit is contained in:
Maxime U. Garcia 2021-11-11 08:58:59 +01:00 committed by GitHub
parent 4bd530135f
commit 3b600af50e
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
34 changed files with 90 additions and 90 deletions

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@ -11,11 +11,11 @@ process GATK4_APPLYBQSR {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_BASERECALIBRATOR {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_BEDTOINTERVALLIST {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

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@ -11,11 +11,11 @@ process GATK4_CALCULATECONTAMINATION {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_CREATESEQUENCEDICTIONARY {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.2.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.2.0--hdfd78af_1"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.2.0--hdfd78af_1"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_FASTQTOSAM {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_FILTERMUTECTCALLS {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_GENOMICSDBIMPORT {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_GETPILEUPSUMMARIES {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_HAPLOTYPECALLER {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_INTERVALLISTTOOLS {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--hdfd78af_1"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--hdfd78af_1"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_LEARNREADORIENTATIONMODEL {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_MARKDUPLICATES {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_MERGEBAMALIGNMENT {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_MERGEVCFS {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_MUTECT2 {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_REVERTSAM {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_SAMTOFASTQ {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_SPLITNCIGARREADS {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -11,11 +11,11 @@ process GATK4_VARIANTFILTRATION {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
}
input:

View file

@ -5,7 +5,7 @@
- gatk4
files:
- path: output/gatk4/test.bam
md5sum: 87a2eabae2b7b41574f966612b5addae
md5sum: af56f5dd81b95070079d54670507f530
- name: gatk4 applybqsr test_gatk4_applybqsr_intervals
command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config
@ -14,7 +14,7 @@
- gatk4
files:
- path: output/gatk4/test.bam
md5sum: 9c015d3c1dbd9eee793b7386f432b6aa
md5sum: 0cbfa4be143e988d56ce741b5077510e
- name: gatk4 applybqsr test_gatk4_applybqsr_cram
command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config
@ -23,4 +23,4 @@
- gatk4
files:
- path: output/gatk4/test.bam
md5sum: 02f84815fdbc99c21c8d42ebdcabbbf7
md5sum: 720ef7453fc3c9def18bbe396062346c

View file

@ -5,7 +5,7 @@
- gatk4
files:
- path: output/gatk4/test.contamination.table
md5sum: ff348a26dd09404239a7ed0da7d98874
md5sum: 5fdcf1728cf98985ce31c038eb24e05c
- 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
@ -14,7 +14,7 @@
- gatk4
files:
- path: output/gatk4/test.contamination.table
md5sum: ff348a26dd09404239a7ed0da7d98874
md5sum: 5fdcf1728cf98985ce31c038eb24e05c
- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation
command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c tests/config/nextflow.config
@ -23,6 +23,6 @@
- gatk4
files:
- path: output/gatk4/test.contamination.table
md5sum: ff348a26dd09404239a7ed0da7d98874
md5sum: 5fdcf1728cf98985ce31c038eb24e05c
- path: output/gatk4/test.segmentation.table
md5sum: 478cb4f69ec001944b9cd0e7e4de01ef
md5sum: 91f28bfe4727a3256810927fc5eba92f

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@ -6,4 +6,4 @@
files:
- path: output/gatk4/test.pon.vcf.gz
- path: output/gatk4/test.pon.vcf.gz.tbi
md5sum: d88d2b745c9226ddf284e3494db8b9d2
md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4

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@ -5,7 +5,7 @@
- gatk4
files:
- path: output/gatk4/test.bam
md5sum: 4967100b2e4912c0e4ce0976d946bafb
md5sum: 0a0d308b219837977b8df9daa26db7de
- 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
@ -14,4 +14,4 @@
- gatk4/fastqtosam
files:
- path: output/gatk4/test.bam
md5sum: 4967100b2e4912c0e4ce0976d946bafb
md5sum: 0a0d308b219837977b8df9daa26db7de

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@ -8,7 +8,7 @@
- path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
md5sum: 98e1b87a52999eb8f429ef4a7877eb3f
- path: output/gatk4/test.filtered.vcf.gz.tbi
md5sum: d88d2b745c9226ddf284e3494db8b9d2
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
@ -20,7 +20,7 @@
- path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
md5sum: 98e1b87a52999eb8f429ef4a7877eb3f
- path: output/gatk4/test.filtered.vcf.gz.tbi
md5sum: d88d2b745c9226ddf284e3494db8b9d2
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
@ -32,4 +32,4 @@
- path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
md5sum: 98e1b87a52999eb8f429ef4a7877eb3f
- path: output/gatk4/test.filtered.vcf.gz.tbi
md5sum: d88d2b745c9226ddf284e3494db8b9d2
md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4

View file

@ -5,7 +5,7 @@
- gatk4/getpileupsummaries
files:
- path: output/gatk4/test.pileups.table
md5sum: 00f92a8f7282d6129f1aca04e2c7d968
md5sum: 0d19674bef2ff0700d5b02b3463dd210
- 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
@ -14,4 +14,4 @@
- gatk4/getpileupsummaries
files:
- path: output/gatk4/test.pileups.table
md5sum: 00f92a8f7282d6129f1aca04e2c7d968
md5sum: 0d19674bef2ff0700d5b02b3463dd210

View file

@ -7,7 +7,7 @@
- path: output/gatk4/test.bai
md5sum: e9c125e82553209933883b4fe2b8d7c2
- path: output/gatk4/test.bam
md5sum: bda9a7bf5057f2288ed70be3eb8a753f
md5sum: f94271007c1ec8e56adfdd8e45a07bd0
- path: output/gatk4/test.metrics
- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
@ -17,7 +17,7 @@
- gatk4
files:
- path: output/gatk4/test.bai
md5sum: d12be29abba5865b7da0cd23f1a84e86
md5sum: bad71df9c876e72a5bc0a3e0fd755f92
- path: output/gatk4/test.bam
md5sum: e988925ed850f8d9d966aa6689ae57de
md5sum: e0462bd4fe2cf4beda71e1bd2c66235b
- path: output/gatk4/test.metrics

View file

@ -5,4 +5,4 @@
- gatk4/mergebamalignment
files:
- path: output/gatk4/test.bam
md5sum: bd4a5e2ea916826aadebb5878333e26f
md5sum: e6f1b343700b7ccb94e81ae127433988

View file

@ -5,7 +5,7 @@
- gatk4
files:
- path: output/gatk4/test.vcf.gz
md5sum: ff48f175e26db2d4b2957762f6d1c715
md5sum: 5b289bda88d3a3504f2e19ee8cff177c
- name: gatk4 mergevcfs test_gatk4_mergevcfs_refdict
command: nextflow run tests/modules/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config
@ -14,4 +14,4 @@
- gatk4
files:
- path: output/gatk4/test.vcf.gz
md5sum: ff48f175e26db2d4b2957762f6d1c715
md5sum: 5b289bda88d3a3504f2e19ee8cff177c

View file

@ -5,4 +5,4 @@
- gatk4/revertsam
files:
- path: output/gatk4/test.reverted.bam
md5sum: f778310b18b83b49929eb648594f96dc
md5sum: f783a88deb45c3a2c20ca12cbe1c5652

View file

@ -5,4 +5,4 @@
- gatk4/splitncigarreads
files:
- path: output/gatk4/test.bam
md5sum: 8d05a41f9467e62d3fc1bc725f0869ec
md5sum: bfe6d04a4072f97fdb97dbc502c9d3e2

View file

@ -31,7 +31,7 @@
contains:
- "FORMAT=<ID=AD,Number=R,Type=Integer,Description="
- path: output/gatk4/test_panel/vidmap.json
md5sum: ee4f6815c433caa8ab101ec45ff328a6
md5sum: ac4e96e03bbbc5c72fac77d487e73d9e
# gatk4 createsomaticpanelofnormals
- path: output/gatk4/test_panel.vcf.gz
- path: output/gatk4/test_panel.vcf.gz.tbi