-
Notifications
You must be signed in to change notification settings - Fork 2
/
run_topsstack.cwl
68 lines (67 loc) · 1.71 KB
/
run_topsstack.cwl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
#!/usr/bin/env cwl-runner
cwlVersion: v1.1
class: CommandLineTool
$namespaces:
cwltool: http://commonwl.org/cwltool#
baseCommand: [sh]
arguments:
- -c
- if [ ! -d $HOME/topsstack_hamsar ]; then cp -r /home/jovyan/topsstack_hamsar $HOME/; fi &&
if [ ! -d $HOME/.ipython ]; then cp -r /home/jovyan/.ipython $HOME/ || true ; fi &&
/opt/conda/bin/papermill $(inputs.input_nb) $(inputs.output_nb)
-p min_lat '$(inputs.min_lat)'
-p max_lat '$(inputs.max_lat)'
-p min_lon '$(inputs.min_lon)'
-p max_lon '$(inputs.max_lon)'
-p master_date '$(inputs.master_date)'
-p start_date '$(inputs.start_date)'
-p end_date '$(inputs.end_date)'
-p track_number '$(inputs.track_number)'
hints:
"cwltool:Secrets":
secrets:
- urs_user
- urs_pass
requirements:
DockerRequirement:
dockerPull: hysds1/topsstack_hamsar:20220121
InitialWorkDirRequirement:
listing:
- entryname: .netrc
entry: |
machine urs.earthdata.nasa.gov login $(inputs.urs_user) password $(inputs.urs_pass)
macdef init
NetworkAccess:
class: NetworkAccess
networkAccess: true
ResourceRequirement:
class: ResourceRequirement
coresMin: 8
# the next 3 are in mebibytes
ramMin: 64000
tmpdirMin: 200000
outdirMin: 100000
inputs:
urs_user: string
urs_pass: string
input_nb: string
output_nb: string
min_lat: float
max_lat: float
min_lon: float
max_lon: float
master_date: string
start_date: string
end_date: string
track_number: int
outputs:
dataset_dir:
type: Directory
outputBinding:
glob: "coregistered_slcs-*"
stdout_file:
type: stdout
stderr_file:
type: stderr
stdout: stdout_run_topsstack.txt
stderr: stderr_run_topsstack.txt