GATK4: GatherBQSRReports¶
Gatk4GatherBQSRReports
· 1 contributor · 4 versions
USAGE: GatherBQSRReports [arguments] Gathers scattered BQSR recalibration reports into a single file Version:4.1.3.0
Quickstart¶
from janis_bioinformatics.tools.gatk4.gatherbqsrreports.versions import Gatk4GatherBQSRReports_4_1_4 wf = WorkflowBuilder("myworkflow") wf.step( "gatk4gatherbqsrreports_step", Gatk4GatherBQSRReports_4_1_4( ) ) wf.output("out", source=gatk4gatherbqsrreports_step.out)
OR
- Install Janis
- Ensure Janis is configured to work with Docker or Singularity.
- Ensure all reference files are available:
Note
More information about these inputs are available below.
- Generate user input files for Gatk4GatherBQSRReports:
# user inputs
janis inputs Gatk4GatherBQSRReports > inputs.yaml
inputs.yaml
{}
- Run Gatk4GatherBQSRReports with:
janis run [...run options] \
--inputs inputs.yaml \
Gatk4GatherBQSRReports
Information¶
ID: | Gatk4GatherBQSRReports |
---|---|
URL: | No URL to the documentation was provided |
Versions: | 4.1.4.0, 4.1.3.0, 4.1.2.0, 4.0.12.0 |
Container: | broadinstitute/gatk:4.1.4.0 |
Authors: | Michael Franklin |
Citations: | None |
Created: | 2020-05-18 |
Updated: | 2020-05-18 |
Outputs¶
name | type | documentation |
---|---|---|
out | tsv |
Additional configuration (inputs)¶
name | type | prefix | position | documentation |
---|---|---|---|---|
javaOptions | Optional<Array<String>> | |||
compression_level | Optional<Integer> | Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2. | ||
reports | Optional<Array<tsv>> | –input | (-I) List of scattered BQSR report files This argument must be specified at least once. Required. | |
outputFilename | Optional<Filename> | –output | (-O) File to output the gathered file to Required. | |
arguments_file | Optional<File> | –arguments_file | read one or more arguments files and add them to the command line This argument may be specified 0 or more times. Default value: null. | |
gatkConfigFile | Optional<String> | –gatk-config-file | A configuration file to use with the GATK. Default value: null. | |
gcsMaxRetries | Optional<Integer> | –gcs-max-retries | (-gcs-retries) If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection Default value: 20. | |
gcsProjectForRequesterPays | Optional<String> | –gcs-project-for-requester-pays | Project to bill when accessing ‘requester pays’ buckets. If unset, these buckets cannot be accessed. Default value: . | |
help | Optional<Boolean> | –help | (-h) display the help message Default value: false. Possible values: {true, false} | |
quiet | Optional<Boolean> | –QUIET | Whether to suppress job-summary info on System.err. Default value: false. Possible values: {true, false} | |
tmpDir | Optional<Boolean> | –tmp-dir | Temp directory to use. Default value: null. | |
useJdkDeflater | Optional<Boolean> | –use-jdk-deflater | (-jdk-deflater) Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false. Possible values: {true, false} | |
useJdkInflater | Optional<Boolean> | –use-jdk-inflater | (-jdk-inflater) Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false. Possible values: {true, false} | |
verbosity | Optional<Boolean> | –verbosity | (-verbosity) Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING, INFO, DEBUG} | |
version | Optional<Boolean> | –version | display the version number for this tool Default value: false. Possible values: {true, false} | |
showhidden | Optional<Boolean> | –showHidden | (-showHidden) display hidden arguments Default value: false. Possible values: {true, false} |
Workflow Description Language¶
version development
task Gatk4GatherBQSRReports {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
Array[String]? javaOptions
Int? compression_level
Array[File]? reports
String? outputFilename
File? arguments_file
String? gatkConfigFile
Int? gcsMaxRetries
String? gcsProjectForRequesterPays
Boolean? help
Boolean? quiet
Boolean? tmpDir
Boolean? useJdkDeflater
Boolean? useJdkInflater
Boolean? verbosity
Boolean? version
Boolean? showhidden
}
command <<<
set -e
gatk GatherBQSRReports \
--java-options '-Xmx~{((select_first([runtime_memory, 4]) * 3) / 4)}G ~{if (defined(compression_level)) then ("-Dsamjdk.compress_level=" + compression_level) else ""} ~{sep(" ", select_first([javaOptions, []]))}' \
~{if (defined(reports) && length(select_first([reports])) > 0) then "--input '" + sep("' --input '", select_first([reports])) + "'" else ""} \
--output '~{select_first([outputFilename, "generated.recal_data.tsv"])}' \
~{if defined(arguments_file) then ("--arguments_file '" + arguments_file + "'") else ""} \
~{if defined(gatkConfigFile) then ("--gatk-config-file '" + gatkConfigFile + "'") else ""} \
~{if defined(gcsMaxRetries) then ("--gcs-max-retries " + gcsMaxRetries) else ''} \
~{if defined(gcsProjectForRequesterPays) then ("--gcs-project-for-requester-pays '" + gcsProjectForRequesterPays + "'") else ""} \
~{if (defined(help) && select_first([help])) then "--help" else ""} \
~{if (defined(quiet) && select_first([quiet])) then "--QUIET" else ""} \
~{if (defined(tmpDir) && select_first([tmpDir])) then "--tmp-dir" else ""} \
~{if (defined(useJdkDeflater) && select_first([useJdkDeflater])) then "--use-jdk-deflater" else ""} \
~{if (defined(useJdkInflater) && select_first([useJdkInflater])) then "--use-jdk-inflater" else ""} \
~{if (defined(verbosity) && select_first([verbosity])) then "--verbosity" else ""} \
~{if (defined(version) && select_first([version])) then "--version" else ""} \
~{if (defined(showhidden) && select_first([showhidden])) then "--showHidden" else ""}
>>>
runtime {
cpu: select_first([runtime_cpu, 1])
disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
docker: "broadinstitute/gatk:4.1.4.0"
duration: select_first([runtime_seconds, 86400])
memory: "~{select_first([runtime_memory, 4])}G"
preemptible: 2
}
output {
File out = select_first([outputFilename, "generated.recal_data.tsv"])
}
}
Common Workflow Language¶
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'GATK4: GatherBQSRReports'
doc: |
USAGE: GatherBQSRReports [arguments]
Gathers scattered BQSR recalibration reports into a single file
Version:4.1.3.0
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: broadinstitute/gatk:4.1.4.0
inputs:
- id: javaOptions
label: javaOptions
type:
- type: array
items: string
- 'null'
- id: compression_level
label: compression_level
doc: |-
Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2.
type:
- int
- 'null'
- id: reports
label: reports
doc: |-
(-I) List of scattered BQSR report files This argument must be specified at least once. Required.
type:
- type: array
inputBinding:
prefix: --input
separate: true
items: File
- 'null'
inputBinding: {}
- id: outputFilename
label: outputFilename
doc: (-O) File to output the gathered file to Required.
type:
- string
- 'null'
default: generated.recal_data.tsv
inputBinding:
prefix: --output
separate: true
- id: arguments_file
label: arguments_file
doc: |-
read one or more arguments files and add them to the command line This argument may be specified 0 or more times. Default value: null.
type:
- File
- 'null'
inputBinding:
prefix: --arguments_file
separate: true
- id: gatkConfigFile
label: gatkConfigFile
doc: 'A configuration file to use with the GATK. Default value: null.'
type:
- string
- 'null'
inputBinding:
prefix: --gatk-config-file
separate: true
- id: gcsMaxRetries
label: gcsMaxRetries
doc: |-
(-gcs-retries) If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection Default value: 20.
type:
- int
- 'null'
inputBinding:
prefix: --gcs-max-retries
separate: true
- id: gcsProjectForRequesterPays
label: gcsProjectForRequesterPays
doc: |2-
Project to bill when accessing 'requester pays' buckets. If unset, these buckets cannot be accessed. Default value: .
type:
- string
- 'null'
inputBinding:
prefix: --gcs-project-for-requester-pays
separate: true
- id: help
label: help
doc: |-
(-h) display the help message Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --help
separate: true
- id: quiet
label: quiet
doc: |-
Whether to suppress job-summary info on System.err. Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --QUIET
separate: true
- id: tmpDir
label: tmpDir
doc: 'Temp directory to use. Default value: null.'
type:
- boolean
- 'null'
inputBinding:
prefix: --tmp-dir
separate: true
- id: useJdkDeflater
label: useJdkDeflater
doc: |-
(-jdk-deflater) Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --use-jdk-deflater
separate: true
- id: useJdkInflater
label: useJdkInflater
doc: |-
(-jdk-inflater) Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --use-jdk-inflater
separate: true
- id: verbosity
label: verbosity
doc: |-
(-verbosity) Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING, INFO, DEBUG}
type:
- boolean
- 'null'
inputBinding:
prefix: --verbosity
separate: true
- id: version
label: version
doc: |-
display the version number for this tool Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --version
separate: true
- id: showhidden
label: showhidden
doc: |-
(-showHidden) display hidden arguments Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --showHidden
separate: true
outputs:
- id: out
label: out
type: File
outputBinding:
glob: generated.recal_data.tsv
loadContents: false
stdout: _stdout
stderr: _stderr
baseCommand:
- gatk
- GatherBQSRReports
arguments:
- prefix: --java-options
position: -1
valueFrom: |-
$("-Xmx{memory}G {compression} {otherargs}".replace(/\{memory\}/g, (([inputs.runtime_memory, 4].filter(function (inner) { return inner != null })[0] * 3) / 4)).replace(/\{compression\}/g, (inputs.compression_level != null) ? ("-Dsamjdk.compress_level=" + inputs.compression_level) : "").replace(/\{otherargs\}/g, [inputs.javaOptions, []].filter(function (inner) { return inner != null })[0].join(" ")))
hints:
- class: ToolTimeLimit
timelimit: |-
$([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: Gatk4GatherBQSRReports