CWL is a programming language created in 2014 by Luka Stojanovic.
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The Common Workflow Language (CWL) is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry.
#!/usr/bin/env cwl-runner
# Originally from
# https://github.com/Duke-GCB/GGR-cwl/blob/54e897263a702ff1074c8ac814b4bf7205d140dd/utils/trunk-peak-score.cwl
# Released under the MIT License:
# https://github.com/Duke-GCB/GGR-cwl/blob/54e897263a702ff1074c8ac814b4bf7205d140dd/LICENSE
# Converted to CWL v1.0 syntax using
# https://github.com/common-workflow-language/cwl-upgrader
# and polished by Michael R. Crusoe <mrc@commonwl.org>
# All modifications also released under the MIT License
cwlVersion: v1.0
class: CommandLineTool
doc: Trunk scores in ENCODE bed6+4 files
hints:
DockerRequirement:
dockerPull: dukegcb/workflow-utils
inputs:
peaks:
type: File
sep:
type: string
default: \t
outputs:
trunked_scores_peaks:
type: stdout
baseCommand: awk
arguments:
- -F $(inputs.sep)
- BEGIN{OFS=FS}$5>1000{$5=1000}{print}
- $(inputs.peaks.path)
stdout: $(inputs.peaks.nameroot).trunked_scores$(inputs.peaks.nameext)
| Feature | Supported | Token | Example |
|---|---|---|---|
| Comments | ✓ | # A comment |
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| Line Comments | ✓ | # | # A comment |
| Semantic Indentation | X |