Given the following workflow (with no inputs)
#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0
inputs: {}
outputs:
- id: output_wf
outputSource: my_first_step/output_log
type: string
steps:
my_first_step:
run:
class: CommandLineTool
requirements:
- class: DockerRequirement
dockerPull: "alpine:latest"
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entryname: run.sh
entry: |
#!/usr/bin/env sh
echo -n "My basic tool"
inputs: {}
stdout: stdout.txt
outputs:
- id: output_log
type: string
outputBinding:
glob: stdout.txt
loadContents: true
outputEval: $(self[0].contents)
baseCommand: sh
arguments:
- run.sh
in: {}
out:
- id: output_log
I can run cwltool --debug and get the following stderr
INFO /home/alexiswl/miniforge3/envs/cwl-ica/bin/cwltool 3.1.20230624081518
INFO Resolved 'foo.cwl' to 'file:///tmp/tmp.HLhGFfydkY/foo.cwl'
DEBUG Parsed job order from command line: {
"id": "foo.cwl"
}
DEBUG [workflow ] initialized from file:///tmp/tmp.HLhGFfydkY/foo.cwl
INFO [workflow ] start
DEBUG [workflow ] inputs {}
INFO [workflow ] starting step my_first_step
DEBUG [step my_first_step] job input {}
DEBUG [step my_first_step] evaluated job input to {}
INFO [step my_first_step] start
DEBUG [job my_first_step] initializing from file:///tmp/tmp.HLhGFfydkY/foo.cwl#my_first_step/9dc27904-2183-4ff2-9a5d-1c6324e4fd4c as part of step my_first_step
DEBUG [job my_first_step] {}
DEBUG [job my_first_step] path mappings is {}
DEBUG [job my_first_step] command line bindings is [
{
"position": [
-1000000,
0
],
"datum": "sh"
},
{
"position": [
0,
0
],
"datum": "run.sh"
}
]
DEBUG [job my_first_step] initial work dir {
"_:c0aaf467-3b9c-4a3d-b29a-7b908b7d58ee": [
"#!/usr/bin/env sh\n\necho -n \"My basic tool\" \n",
"/tdidkb/run.sh",
"CreateFile",
true
]
}
INFO [job my_first_step] /tmp/befv48p7$ docker \
run \
-i \
--mount=type=bind,source=/tmp/befv48p7,target=/tdidkb \
--mount=type=bind,source=/tmp/vo8g7cmc,target=/tmp \
--workdir=/tdidkb \
--read-only=true \
--log-driver=none \
--user=1000:1000 \
--rm \
--cidfile=/tmp/lt90ptqs/20230703210305-792241.cid \
--env=TMPDIR=/tmp \
--env=HOME=/tdidkb \
alpine:latest \
sh \
run.sh > /tmp/befv48p7/stdout.txt
INFO [job my_first_step] Max memory used: 0MiB
INFO [job my_first_step] completed success
DEBUG [job my_first_step] outputs {
"output_log": "My basic tool"
}
DEBUG [step my_first_step] produced output {
"file:///tmp/tmp.HLhGFfydkY/foo.cwl#my_first_step/output_log": "My basic tool"
}
INFO [step my_first_step] completed success
INFO [workflow ] completed success
DEBUG [workflow ] outputs {
"output_wf": "My basic tool"
}
DEBUG [job my_first_step] Removing input staging directory /tmp/xncm59_2
DEBUG [job my_first_step] Removing temporary directory /tmp/vo8g7cmc
DEBUG Removing intermediate output directory /tmp/0npdrra0
DEBUG Removing intermediate output directory /tmp/befv48p7
INFO Final process status is success
Wondering if anyone has already worked on something to convert this into digestible format.
Might look something like
{
"steps": [
{
"id": "my_first_step",
"initialworkdirfiles": [
{
"_:c0aaf467-3b9c-4a3d-b29a-7b908b7d58ee": [
"#!/usr/bin/env sh\n\necho -n \"My basic tool\" \n",
"/tdidkb/run.sh",
"CreateFile",
true
]
}
],
"commandLineBindings": [
{
"position": [
-1000000,
0
],
"datum": "sh"
},
{
"position": [
0,
0
],
"datum": "run.sh"
}
],
"dockerCommand": [
"docker",
"run",
"-i",
"--mount=type=bind,source=/tmp/befv48p7,target=/tdidkb",
"--mount=type=bind,source=/tmp/vo8g7cmc,target=/tmp",
"--workdir=/tdidkb",
"--read-only=true",
"--log-driver=none",
"--user=1000:1000",
"--rm",
"--cidfile=/tmp/lt90ptqs/20230703210305-792241.cid",
"--env=TMPDIR=/tmp",
"--env=HOME=/tdidkb",
"alpine:latest",
"sh",
"run.sh"
]
}
]
}