执行工作流：cwltool /home/zcy/download/cwl/wf.cwl /home/zcy/download/cwl/echo-job.yml
wf.cwl
cwlVersion: v1.2
class: Workflow
inputs:
message: string
outputs:
out:
type: File
outputSource: uppercase/example_out
steps:
echo:
run: /home/zcy/download/cwl/zzz_print.cwl
in:
message: message
out: [out]
uppercase:
run: /home/zcy/download/cwl/ccc.cwl
in:
mypath:
source: echo/out
out: [example_out]
echo-job.yml
message: Hello world!
zzz_print.cwl
cwlVersion: v1.0
class: CommandLineTool
stdout: tst_stdout.txt
baseCommand: [python, /home/zcy/download/cwl/input/zzz_print.py]
inputs:
message:
type: string
inputBinding:
position: 1
outputs:
out:
type: string
outputBinding:
glob: tst_stdout.txt
loadContents: true
outputEval: $(self[0].contents)
zzz_print.py
import argparse
parser = argparse.ArgumentParser(description='download files by ftp')
parser.add_argument('message', type=str, help='PDB')
def tst(args):
with open('/home/zzz_print.out', 'w') as f:
f.write(args)
print('/home/zzz_print.out')
if __name__ == '__main__':
args = parser.parse_args()
tst(args.message)
ccc.cwl
cwlVersion: v1.0
class: CommandLineTool
baseCommand: [python, /home/zcy/download/cwl/input/ccc.py]
inputs:
mypath:
type: string
inputBinding:
position: 1
outputs:
example_out:
type: stdout
stdout: output_ccc.txt
ccc.py
import argparse
parser = argparse.ArgumentParser(description='download files by ftp')
parser.add_argument('mypath', type=str, help='PDB')
def tst(args):
fpath = args.split(None)[0]
with open(fpath, 'r') as f:
data = f.read()
print('final result:')
print(data)
if __name__ == '__main__':
args = parser.parse_args()
tst(args.mypath)
标签：__,args,笔记,学习,cwl,cwltoo,print,download,out From： https://www.cnblogs.com/testzcy/p/17648713.html