MD5 Sum¶
md5sum
· 0 contributors · 1 version
Compute the MD5 message digest of the given file.
Quickstart¶
from janis_unix.tools.md5sum import MD5Sum wf = WorkflowBuilder("myworkflow") wf.step( "md5sum_step", MD5Sum( input_file=None, ) ) wf.output("out", source=md5sum_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 md5sum:
# user inputs
janis inputs md5sum > inputs.yaml
inputs.yaml
input_file: input_file
- Run md5sum with:
janis run [...run options] \
--inputs inputs.yaml \
md5sum
Information¶
ID: | md5sum |
---|---|
URL: | No URL to the documentation was provided |
Versions: | v1.0.0 |
Container: | ubuntu@sha256:1d7b639619bdca2d008eca2d5293e3c43ff84cbee597ff76de3b7a7de3e84956 |
Authors: | |
Citations: | None |
Created: | None |
Updated: | 2020-06-09 00:00:00 |
Outputs¶
name | type | documentation |
---|---|---|
out | stdout<File> |
Additional configuration (inputs)¶
name | type | prefix | position | documentation |
---|---|---|---|---|
input_file | File | 1 |
Workflow Description Language¶
version development
task md5sum {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
File input_file
}
command <<<
set -e
md5sum \
'~{input_file}' \
| awk '{print $1}'
>>>
runtime {
cpu: select_first([runtime_cpu, 1])
disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
docker: "ubuntu@sha256:1d7b639619bdca2d008eca2d5293e3c43ff84cbee597ff76de3b7a7de3e84956"
duration: select_first([runtime_seconds, 86400])
memory: "~{select_first([runtime_memory, 4])}G"
preemptible: 2
}
output {
File out = stdout()
}
}
Common Workflow Language¶
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: MD5 Sum
doc: Compute the MD5 message digest of the given file.
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: ubuntu@sha256:1d7b639619bdca2d008eca2d5293e3c43ff84cbee597ff76de3b7a7de3e84956
inputs:
- id: input_file
label: input_file
type: File
inputBinding:
position: 1
outputs:
- id: out
label: out
type: stdout
stdout: _stdout
stderr: _stderr
baseCommand: md5sum
arguments:
- position: 2
valueFrom: "| awk '{print $1}'"
shellQuote: false
hints:
- class: ToolTimeLimit
timelimit: |-
$([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: md5sum