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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
id: generic_step
requirements:
- class: InlineJavascriptRequirement
baseCommand:
- python3
arguments:
- prefix: -c
valueFrom: |
import sys
true = True
false = False
null = None
steps_list = $(inputs.steps)
steps_id_list = list(map(lambda item: item['step_id'], steps_list))
for step in steps_list:
try:
step_id = step.get('step_id')
step_type = step.get('step_type')
parameters = step.get('parameters')
line = '.'.join([step_id, 'type'])
line += '=%s' % step_type
print(line)
for parameter_name, parameter in parameters.items():
if isinstance(parameter, dict):
if parameter['class'] in ['File', 'Directory']:
parameter = parameter['basename']
else:
raise NotImplemented()
if parameter is None:
continue
line = '.'.join([step_id, parameter_name])
line = '%s=%s' % (line, parameter)
print(line)
except KeyError as e:
print('invalid input for step ', step, ':', e)
sys.exit(1)
last_step_line = 'steps=[%s,count]' % ', '.join(steps_id_list)
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print(last_step_line)
inputs:
- id: steps
type: Any[]?
outputs:
- id: parset
doc: Parset output file
type: File
outputBinding:
glob: parset
- id: input_files
doc: additional input files
type: File[]
outputBinding:
outputEval: |-
${
var outfiles = []
for(var step in inputs.steps){
step = inputs.steps[step]
for(var parameter in step['parameters']){
parameter = step['parameters'][parameter]
if (parameter != null && parameter.class =='File'){
outfiles.push(parameter)
}
}
}
return outfiles
}
- id: input_directories
doc: additional input directory
type: Directory[]
outputBinding:
outputEval: |
${
var outdirs = []
for(var step in inputs.steps){
step = inputs.steps[step]
for(var parameter in step['parameters']){
parameter = step['parameters'][parameter]
if (parameter != null && parameter.class=='Directory'){
outdirs.push(parameter)
}
}
}
return outdirs
}
- id: output_file_names
doc: expected output files
type: Any
outputBinding:
outputEval: |
${
var out_names = {}
for(var step_idx in inputs.steps){
var step = inputs.steps[step_idx]
var step_id = step['step_id']
var step_dirs = {}
if(!step.hasOwnProperty("output_files")) continue;
var step_files = {}
for(var index in step['output_files']){
var file_id = index
var file_name = step['output_files'][file_id]
step_files[file_id] = file_name
}
out_names[step_id] = step_files
}
return out_names
}
- id: output_directory_names
doc: expected output directories
type: Any
outputBinding:
outputEval: |-
${
var out_names = {}
for(var step_idx in inputs.steps){
var step = inputs.steps[step_idx]
var step_id = step['step_id']
var step_dirs = {}
if(!step.hasOwnProperty("output_directories")) continue;
for(var index in step['output_directories']){
var file_id = index
var file_name = step['output_directories'][file_id]
step_dirs[file_id] = file_name
}
out_names[step_id] = step_dirs
}
return out_names
}
stdout:
parset