SamTools: faidx¶
SamToolsFaidx
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Quickstart¶
from janis_bioinformatics.tools.samtools.faidx.versions import SamToolsFaidx_1_9 wf = WorkflowBuilder("myworkflow") wf.step( "samtoolsfaidx_step", SamToolsFaidx_1_9( reference=None, ) ) wf.output("out", source=samtoolsfaidx_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 SamToolsFaidx:
# user inputs
janis inputs SamToolsFaidx > inputs.yaml
inputs.yaml
reference: reference.fasta
- Run SamToolsFaidx with:
janis run [...run options] \
--inputs inputs.yaml \
SamToolsFaidx
Information¶
ID: | SamToolsFaidx |
---|---|
URL: | http://www.htslib.org/doc/samtools.html#COMMANDS_AND_OPTIONS |
Versions: | 1.9.0, 1.7.0 |
Container: | quay.io/biocontainers/samtools:1.9–h8571acd_11 |
Authors: | Michael Franklin |
Citations: | None |
Created: | 2020-02-14 |
Updated: | 2020-02-14 |
Outputs¶
name | type | documentation |
---|---|---|
out | FastaFai |
Additional configuration (inputs)¶
name | type | prefix | position | documentation |
---|---|---|---|---|
reference | Fasta | 1 |
Workflow Description Language¶
version development
task SamToolsFaidx {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
File reference
}
command <<<
set -e
cp -f '~{reference}' '.'
samtools faidx \
'~{basename(reference)}'
>>>
runtime {
cpu: select_first([runtime_cpu, 1])
disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
docker: "quay.io/biocontainers/samtools:1.9--h8571acd_11"
duration: select_first([runtime_seconds, 86400])
memory: "~{select_first([runtime_memory, 4])}G"
preemptible: 2
}
output {
File out = basename(reference)
File out_fai = basename(reference) + ".fai"
}
}
Common Workflow Language¶
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'SamTools: faidx'
doc: ''
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.reference)
- class: DockerRequirement
dockerPull: quay.io/biocontainers/samtools:1.9--h8571acd_11
inputs:
- id: reference
label: reference
type: File
inputBinding:
position: 1
outputs:
- id: out
label: out
type: File
secondaryFiles:
- pattern: .fai
outputBinding:
glob: $(inputs.reference.basename)
loadContents: false
stdout: _stdout
stderr: _stderr
baseCommand:
- samtools
- faidx
arguments: []
hints:
- class: ToolTimeLimit
timelimit: |-
$([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: SamToolsFaidx