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refactor config-tag-mdp #149

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Aug 5, 2024
Merged

refactor config-tag-mdp #149

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35 changes: 0 additions & 35 deletions utils/config-tag-mdp-plugin/tests/test_config_tag_mdp.py
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0 utils/config-tag-mdp-plugin/.bumpversion.cfg → ...mics/config-tag-mdp-tool/.bumpversion.cfg
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0 utils/config-tag-mdp-plugin/.dockerignore → ...ynamics/config-tag-mdp-tool/.dockerignore
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0 utils/config-tag-mdp-plugin/.gitignore → ...r-dynamics/config-tag-mdp-tool/.gitignore
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0 utils/config-tag-mdp-plugin/CHANGELOG.md → ...dynamics/config-tag-mdp-tool/CHANGELOG.md
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0 utils/config-tag-mdp-plugin/README.md → ...ar-dynamics/config-tag-mdp-tool/README.md
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0 utils/config-tag-mdp-plugin/VERSION → ...ular-dynamics/config-tag-mdp-tool/VERSION
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53 changes: 53 additions & 0 deletions utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow.cwl
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#!/usr/bin/env cwl-runner
# This file was autogenerated using the Workflow Inference Compiler, version 0+unknown
# https://github.com/PolusAI/workflow-inference-compiler
steps:
- id: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0
in:
config:
source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config
dt:
source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt
nsteps:
source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps
ref_p:
source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p
ref_t:
source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t
out:
- output_config_string
run: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]
cwlVersion: v1.2
class: Workflow
$namespaces:
edam: https://edamontology.org/
$schemas:
- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
inputs:
config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config:
type: string
format: edam:format_2330
label: A dictionary of the given arguments as a JSON-encoded string.
doc: A dictionary of the given arguments as a JSON-encoded string.
config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt:
type: float
label: The length of each timestep
doc: The length of each timestep
config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps:
type: int
label: The number of timesteps
doc: The number of timesteps
config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p:
type: float
label: The nominal pressure
doc: The nominal pressure
config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t:
type: float
label: The nominal temperature
doc: The nominal temperature
outputs:
config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___output_config_string:
type: string
label: A dictionary of the given arguments as a JSON-encoded string.
doc: A dictionary of the given arguments as a JSON-encoded string.
outputSource: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/output_config_string
50 changes: 50 additions & 0 deletions ...generated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]
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#!/usr/bin/env cwl-runner
# This file was autogenerated using the Workflow Inference Compiler, version 0+unknown
# https://github.com/PolusAI/workflow-inference-compiler
class: CommandLineTool
cwlVersion: v1.0
label: Returns a dictionary of the given arguments as a JSON-encoded string.
doc: Returns a dictionary of the given arguments as a JSON-encoded string.
baseCommand: echo
requirements:
InlineJavascriptRequirement: {}
inputs:
config:
label: A dictionary of the given arguments as a JSON-encoded string.
doc: A dictionary of the given arguments as a JSON-encoded string.
type: string
format: edam:format_2330
default: '{}'
nsteps:
label: The number of timesteps
doc: The number of timesteps
type: int
dt:
label: The length of each timestep
doc: The length of each timestep
type: float
ref_t:
label: The nominal temperature
doc: The nominal temperature
type: float
ref_p:
label: The nominal pressure
doc: The nominal pressure
type: float
outputs:
output_config_string:
label: A dictionary of the given arguments as a JSON-encoded string.
doc: A dictionary of the given arguments as a JSON-encoded string.
type: string
outputBinding:
outputEval: "${\n var config = JSON.parse(inputs.config);\n if ((\"mdp\" in\
\ config) === false) {\n config[\"mdp\"] = {}; // Initialize it\n }\n\
\ // TODO: Check for duplicate keys, i.e.\n // \"Pressure coupling incorrect\
\ number of values (I need exactly 1)\"\n config[\"mdp\"][\"nsteps\"] = inputs.nsteps;\n\
\ config[\"mdp\"][\"dt\"] = inputs.dt;\n config[\"mdp\"][\"ref-t\"] = inputs[\"\
ref-t\"]; //Javascript interprets dash as subtract...\n config[\"mdp\"][\"\
ref-p\"] = inputs[\"ref-p\"];\n return JSON.stringify(config);\n}\n"
$namespaces:
edam: https://edamontology.org/
$schemas:
- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
3 changes: 3 additions & 0 deletions ...ed/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0_inputs.yml
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# This file was autogenerated using the Workflow Inference Compiler, version 0+unknown
# https://github.com/PolusAI/workflow-inference-compiler
{}
12 changes: 12 additions & 0 deletions ...s/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow_inputs.yml
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# This file was autogenerated using the Workflow Inference Compiler, version 0+unknown
# https://github.com/PolusAI/workflow-inference-compiler
config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config: '"{\"mdp\": {\"integrator\":
\"md\", \"rvdw\": 1.0, \"rcoulomb\": 1.0, \"coulombtype\": \"PME\",
\"tc-grps\": \"system\", \"tau-t\": 2, \"constraints\": \"h-bonds\",
\"nstxout\": 1000, \"nstenergy\": 1000, \"pcoupl\": \"Parrinello-Rahman\",
\"tau-p\": 1, \"compressibility\": 4.5e-5, \"comm-mode\": \"Linear\",
\"comm-grps\": \"system\"}}"'
config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt: 0.02
config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps: 10000
config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p: 1.0
config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t: 298.0
1 change: 1 addition & 0 deletions ...s/molecular-dynamics/config-tag-mdp-tool/cachedir/4cc56456b99cd83771068ac7c958a576.status
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permanentFail
4 changes: 2 additions & 2 deletions .../config-tag-mdp-plugin/config_tag_mdp.cwl → ...fig-tag-mdp-tool/config_tag_mdp_0@[email protected]
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Expand Up @@ -33,13 +33,13 @@ inputs:
The length of each timestep
type: float

ref-t:
ref_t:
label: The nominal temperature
doc: |-
The nominal temperature
type: float

ref-p:
ref_p:
label: The nominal pressure
doc: |-
The nominal pressure
Expand Down
6 changes: 3 additions & 3 deletions utils/config-tag-mdp-plugin/ict.yml → ...ular-dynamics/config-tag-mdp-tool/ict.yml
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@@ -1,12 +1,12 @@
specVersion: "0.1.0"
name: config_tag_mdp
version: 0.1.0
container: config-tag-mdp-plugin
container: config-tag-mdp-tool
entrypoint:
title: config_tag_mdp
description: Returns a dictionary of the given arguments as a JSON-encoded string.
author: Data Scientist
contact: [email protected]
author: Brandon Walker, Nazanin Donyapour
contact: [email protected], [email protected]
repository:
documentation:
citation:
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3 changes: 3 additions & 0 deletions utils/molecular-dynamics/config-tag-mdp-tool/output_config_tag_mdp_workflow.json
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{
"config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___output_config_string": null
}
6 changes: 6 additions & 0 deletions utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/bag-info.txt
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Bag-Software-Agent: cwltool 3.1.20240404144621
BagIt-Profile-Identifier: https://w3id.org/ro/bagit/profile
Bagging-Date: 2024-07-30
External-Description: Research Object of CWL workflow run
External-Identifier: arcp://uuid,9a41dad8-a1b5-4a5d-825b-437da47258d6/
Payload-Oxum: 510.1
2 changes: 2 additions & 0 deletions utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/bagit.txt
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BagIt-Version: 0.97
Tag-File-Character-Encoding: UTF-8
1 change: 1 addition & 0 deletions ...-tool/provenance/config_tag_mdp_workflow/data/dc/dc0dbba18d47b040109f16862d39de918039856d
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"{\"mdp\": {\"integrator\": \"md\", \"rvdw\": 1.0, \"rcoulomb\": 1.0, \"coulombtype\": \"PME\", \"tc-grps\": \"system\", \"tau-t\": 2, \"constraints\": \"h-bonds\", \"nstxout\": 1000, \"nstenergy\": 1000, \"pcoupl\": \"Parrinello-Rahman\", \"tau-p\": 1, \"compressibility\": 4.5e-5, \"comm-mode\": \"Linear\", \"comm-grps\": \"system\"}}"
1 change: 1 addition & 0 deletions ...lecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/manifest-sha1.txt
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dc0dbba18d47b040109f16862d39de918039856d data/dc/dc0dbba18d47b040109f16862d39de918039856d
13 changes: 13 additions & 0 deletions ...nce/config_tag_mdp_workflow/metadata/logs/engine.49b7c1d9-09c2-4607-b6de-a68051d1aaca.txt
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[2024-07-30T18:16:05,559.492588Z] [cwltool] /home/walkerbd/miniconda3/envs/wic_github_actions/bin/cwltool_filterlog --disable-pull --cachedir cachedir --provenance provenance/config_tag_mdp_workflow --write-summary output_config_tag_mdp_workflow.json --skip-schemas --relax-path-checks --leave-outputs autogenerated/config_tag_mdp_workflow.cwl autogenerated/config_tag_mdp_workflow_inputs.yml
[2024-07-30T18:16:07,64.969540Z] [workflow ] start
[2024-07-30T18:16:07,65.366507Z] [workflow ] starting step config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0
[2024-07-30T18:16:07,65.612078Z] [step config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] start
[2024-07-30T18:16:07,66.546917Z] [job config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] Output of job will be cached in /home/walkerbd/mm-tools/utils/molecular-dynamics/config-tag-mdp-tool/cachedir/4cc56456b99cd83771068ac7c958a576
[2024-07-30T18:16:07,67.748308Z] [job config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] /home/walkerbd/mm-tools/utils/molecular-dynamics/config-tag-mdp-tool/cachedir/4cc56456b99cd83771068ac7c958a576$ echo
[2024-07-30T18:16:07,308.171272Z] [job config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] Job error:
('Error collecting output for parameter \'output_config_string\': autogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: Expression evaluation error:\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: Expecting value: line 1 column 1 (char 0)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: script was:\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 01 "use strict";\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 02 var inputs = {\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 03 "config": "\\"{\\\\\\"mdp\\\\\\": {\\\\\\"integrator\\\\\\": \\\\\\"md\\\\\\", \\\\\\"rvdw\\\\\\": 1.0, \\\\\\"rcoulomb\\\\\\": 1.0, \\\\\\"coulombtype\\\\\\": \\\\\\"PME\\\\\\", \\\\\\"tc-grps\\\\\\": \\\\\\"system\\\\\\", \\\\\\"tau-t\\\\\\": 2, \\\\\\"constraints\\\\\\": \\\\\\"h-bonds\\\\\\", \\\\\\"nstxout\\\\\\": 1000, \\\\\\"nstenergy\\\\\\": 1000, \\\\\\"pcoupl\\\\\\": \\\\\\"Parrinello-Rahman\\\\\\", \\\\\\"tau-p\\\\\\": 1, \\\\\\"compressibility\\\\\\": 4.5e-5, \\\\\\"comm-mode\\\\\\": \\\\\\"Linear\\\\\\", \\\\\\"comm-grps\\\\\\": \\\\\\"system\\\\\\"}}\\"",\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 04 "dt": 0.02,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 05 "nsteps": 10000,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 06 "ref_p": 1.0,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 07 "ref_t": 298.0\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 08 };\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 09 var self = [];\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 10 var runtime = {\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 11 "cores": 1,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 12 "ram": 1024,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 13 "tmpdirSize": 1024,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 14 "outdirSize": 1024,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 15 "tmpdir": "/tmp/belht484",\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 16 "outdir": "/home/walkerbd/mm-tools/utils/molecular-dynamics/config-tag-mdp-tool/cachedir/4cc56456b99cd83771068ac7c958a576"\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 17 };\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 18 (function(){\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 19 var config = JSON.parse(inputs.config);\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 20 if (("mdp" in config) === false) {\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 21 config["mdp"] = {}; // Initialize it\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 22 }\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 23 // TODO: Check for duplicate keys, i.e.\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 24 // "Pressure coupling incorrect number of values (I need exactly 1)"\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 25 config["mdp"]["nsteps"] = inputs.nsteps;\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 26 config["mdp"]["dt"] = inputs.dt;\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 27 config["mdp"]["ref-t"] = inputs["ref-t"]; //Javascript interprets dash as subtract...\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 28 config["mdp"]["ref-p"] = inputs["ref-p"];\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 29 return JSON.stringify(config);\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 30 })()\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: stdout was: \'\'\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: stderr was: \'evalmachine.<anonymous>:20\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: if (("mdp" in config) === false) {\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: ^\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: \nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: TypeError: Cannot use \'in\' operator to search for \'mdp\' in {"mdp": {"integrator": "md", "rvdw": 1.0, "rcoulomb": 1.0, "coulombtype": "PME", "tc-grps": "system", "tau-t": 2, "constraints": "h-bonds", "nstxout": 1000, "nstenergy": 1000, "pcoupl": "Parrinello-Rahman", "tau-p": 1, "compressibility": 4.5e-5, "comm-mode": "Linear", "comm-grps": "system"}}\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: at evalmachine.<anonymous>:20:14\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: at evalmachine.<anonymous>:30:3\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: at Script.runInContext (node:vm:148:12)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: at Script.runInNewContext (node:vm:153:17)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: at Object.runInNewContext (node:vm:309:38)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: at Socket.<anonymous> ([eval]:11:57)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: at Socket.emit (node:events:520:28)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: at addChunk (node:internal/streams/readable:559:12)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: at readableAddChunkPushByteMode (node:internal/streams/readable:510:3)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: at Readable.push (node:internal/streams/readable:390:5)\'', {})
[2024-07-30T18:16:07,308.703661Z] [job config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] completed permanentFail
[2024-07-30T18:16:07,308.988571Z] [step config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] Output is missing expected field file:///home/walkerbd/mm-tools/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow.cwl#config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/output_config_string
[2024-07-30T18:16:07,309.092522Z] [step config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] completed permanentFail
[2024-07-30T18:16:07,309.232473Z] [workflow ] completed permanentFail
[2024-07-30T18:16:07,350.886106Z] Final process status is permanentFail
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