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Commit c1b8db5d authored by Mattia Mancini's avatar Mattia Mancini
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Merge branch 'master' of git.astron.nl:eosc/prefactor3-cwl

parents ed8804f7 302d2799
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1 merge request!69Change the name of the pre-calibrated output MS
Pipeline #227 failed
...@@ -9,15 +9,10 @@ stages: ...@@ -9,15 +9,10 @@ stages:
- test_steps - test_steps
- integration_test - integration_test
before_script: before_script:
# - python3 -V # Print out python version for debugging # make toil workdir
# - apt-get update && apt-get install -y nodejs python3-pip - mkdir workdir
# - python3 -m pip install cwltool cwl-runner - mkdir logs
# - cd test_data
# - tar -xf ${TEST_DATASET_NAME}
# - cd $CI_PROJECT_DIR
# - source /opt/bashrc
after_script: after_script:
- echo "All done" - echo "All done"
...@@ -50,7 +45,7 @@ parset_selector: ...@@ -50,7 +45,7 @@ parset_selector:
stage: test_steps stage: test_steps
allow_failure: true allow_failure: true
script: script:
- cwl-runner steps/DP3.ParsetSelector.cwl test_jobs/parset_selector.json - cwl-runner steps/DP3.Selector.cwl test_jobs/selector.json
file_selector: file_selector:
stage: test_steps stage: test_steps
...@@ -117,8 +112,12 @@ prefactor_calibrator: ...@@ -117,8 +112,12 @@ prefactor_calibrator:
script: script:
- cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH prefactor_calibrator.cwl test_jobs/integration_test_prefactor_calibrator.json - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH prefactor_calibrator.cwl test_jobs/integration_test_prefactor_calibrator.json
toil:
stage: integration_test
script:
- toil-cwl-runner --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH --jobStore jobstore --writeLogs logs --workDir workdir prefactor_calibrator.cwl test_jobs/integration_test_prefactor_calibrator.json
flag_average: flag_average:
stage: integration_test stage: integration_test
script: script:
- cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH test_workflow/flag_average.cwl test_jobs/flag_average.json - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH test_workflow/flag_average.cwl test_jobs/flag_average.json
...@@ -88,12 +88,19 @@ RUN mkdir /home/lofaruser/ && \ ...@@ -88,12 +88,19 @@ RUN mkdir /home/lofaruser/ && \
useradd --no-log-init -r -g lofaruser lofaruser && \ useradd --no-log-init -r -g lofaruser lofaruser && \
chown lofaruser:lofaruser /home/lofaruser chown lofaruser:lofaruser /home/lofaruser
ARG TOIL_VERSION=3.20.0
LABEL toil.version=${TOIL_VERSION}
ARG LSMTool_TAG=master ARG LSMTool_TAG=master
LABEL LSMTool.version.tag=${LSMTool_TAG}
ARG LoSoTo_TAG=master
LABEL LoSoTo.version.tag=${LoSoTo_TAG}
RUN apt-get update && apt-get install -y nodejs python3-pip git wsclean RUN apt-get update && apt-get install -y nodejs python3-pip git wsclean
RUN python3 -m pip install cwltool cwl-runner -e "git://github.com/darafferty/LSMTool.git@${LSMTool_TAG}#egg=LSMTool" git+https://github.com/DataBiosphere/toil RUN python3 -m pip install cwltool cwl-runner -e "git://github.com/darafferty/LSMTool.git@${LSMTool_TAG}#egg=LSMTool" toil[cwl]==${TOIL_VERSION}
RUN python3 -m pip install git+https://github.com/revoltek/losoto.git RUN python3 -m pip install -e "git+https://github.com/revoltek/losoto.git@${LoSoTo_TAG}#egg=LoSoTo"
ADD L570745_uv_first10.MS.tar.xz /data ADD L570745_uv_first10.MS.tar.xz /data
ADD skymodels.tar.gz /data/skymodels ADD skymodels.tar.gz /data/skymodels
......
...@@ -6,13 +6,16 @@ git_clone_or_pull () { ...@@ -6,13 +6,16 @@ git_clone_or_pull () {
BRANCH=$2 BRANCH=$2
DIR=$3 DIR=$3
git clone -single-branch -b "${BRANCH}" "${REPO}" "${DIR}" 2> /dev/null || git -C "${DIR}" pull git clone --single-branch -b "${BRANCH}" "${REPO}" "${DIR}" 2> /dev/null || git -C "${DIR}" pull
} }
# SOFTWARE VERSIONS # SOFTWARE VERSIONS
DP3_TAG=v4.1 DP3_TAG=v4.1
IDG_TAG=0.6 IDG_TAG=0.6
LSMTool_TAG=v1.4.2 LSMTool_TAG=v1.4.2
LoSoTo_TAG=f0398b
TOIL_VERSION=3.20.0
# FETCHES THE IDG # FETCHES THE IDG
git_clone_or_pull https://gitlab.com/astron-idg/idg/ ${IDG_TAG} idg git_clone_or_pull https://gitlab.com/astron-idg/idg/ ${IDG_TAG} idg
...@@ -29,4 +32,9 @@ SCRIPT_PATH=$(realpath ${BASH_SOURCE[0]}) ...@@ -29,4 +32,9 @@ SCRIPT_PATH=$(realpath ${BASH_SOURCE[0]})
DOCKER_PATH=$(dirname ${SCRIPT_PATH}) DOCKER_PATH=$(dirname ${SCRIPT_PATH})
docker build ${DOCKER_PATH} --build-arg=IDG_TAG=${IDG_TAG} --build-arg=DP3_TAG=${DP3_TAG} --build-arg=LSMTool_TAG=${LSMTool_TAG} -t lofareosc/prefactor-ci docker build ${DOCKER_PATH} --build-arg=IDG_TAG=${IDG_TAG}\
--build-arg=DP3_TAG=${DP3_TAG}\
--build-arg=LSMTool_TAG=${LSMTool_TAG}\
--build-arg=LoSoTo_TAG=${LoSoTo_TAG}\
--build-arg=TOIL_VERSION=${TOIL_VERSION}\
-t lofareosc/prefactor-ci
...@@ -5,7 +5,7 @@ cwlVersion: v1.0 ...@@ -5,7 +5,7 @@ cwlVersion: v1.0
id: aoflagger_step_generator id: aoflagger_step_generator
inputs: inputs:
- id: parameters_input - id: steps
type: Any[]? type: Any[]?
default: [] default: []
- id: step_name - id: step_name
...@@ -83,9 +83,9 @@ inputs: ...@@ -83,9 +83,9 @@ inputs:
default: true default: true
doc: Write the quality statistics? doc: Write the quality statistics?
outputs: outputs:
- id: parameters_out - id: augmented_steps
outputSource: outputSource:
- DP3_GenericStep/parameters_out - DP3_GenericStep/augmented_steps
type: Any[] type: Any[]
steps: steps:
...@@ -95,8 +95,8 @@ steps: ...@@ -95,8 +95,8 @@ steps:
default: 'aoflagger' default: 'aoflagger'
- id: step_id - id: step_id
source: step_name source: step_name
- id: parameters_input - id: steps
source: parameters_input source: steps
- id: parameters - id: parameters
valueFrom: $(inputs) valueFrom: $(inputs)
- id: count.save - id: count.save
...@@ -124,7 +124,7 @@ steps: ...@@ -124,7 +124,7 @@ steps:
- id: keepstatistics - id: keepstatistics
source: keepstatistics source: keepstatistics
out: out:
- parameters_out - augmented_steps
run: ../steps/DP3.GenericStep.cwl run: ../steps/DP3.GenericStep.cwl
requirements: requirements:
- class: StepInputExpressionRequirement - class: StepInputExpressionRequirement
......
...@@ -5,7 +5,7 @@ cwlVersion: v1.0 ...@@ -5,7 +5,7 @@ cwlVersion: v1.0
id: average_step_generator id: average_step_generator
inputs: inputs:
- id: input_parset - id: steps
type: Any[]? type: Any[]?
default: [] default: []
- id: step_name - id: step_name
...@@ -48,9 +48,9 @@ inputs: ...@@ -48,9 +48,9 @@ inputs:
<step>.freqstep <step>.freqstep
default: 0 default: 0
outputs: outputs:
- id: parameters_out - id: augmented_steps
outputSource: outputSource:
- DP3_GenericStep/parameters_out - DP3_GenericStep/augmented_steps
type: Any[] type: Any[]
steps: steps:
...@@ -60,8 +60,8 @@ steps: ...@@ -60,8 +60,8 @@ steps:
default: 'averager' default: 'averager'
- id: step_id - id: step_id
source: step_name source: step_name
- id: parameters_input - id: steps
source: input_parset source: steps
- id: parameters - id: parameters
valueFrom: $(inputs) valueFrom: $(inputs)
- id: timestep - id: timestep
...@@ -77,7 +77,7 @@ steps: ...@@ -77,7 +77,7 @@ steps:
- id: freqresolution - id: freqresolution
source: freqresolution source: freqresolution
out: out:
- parameters_out - augmented_steps
run: ../steps/DP3.GenericStep.cwl run: ../steps/DP3.GenericStep.cwl
requirements: requirements:
- class: StepInputExpressionRequirement - class: StepInputExpressionRequirement
......
...@@ -7,7 +7,7 @@ $namespaces: ...@@ -7,7 +7,7 @@ $namespaces:
id: demix_step_generator id: demix_step_generator
inputs: inputs:
- id: parameters_input - id: steps
type: Any[]? type: Any[]?
default: [] default: []
- id: step_name - id: step_name
...@@ -126,16 +126,16 @@ inputs: ...@@ -126,16 +126,16 @@ inputs:
type: int type: int
doc: Maximum number of iterations used in the LM solve doc: Maximum number of iterations used in the LM solve
outputs: outputs:
- id: parameters_out - id: augmented_steps
outputSource: outputSource:
- DP3_GenericStep/parameters_out - DP3_GenericStep/augmented_steps
type: Any[] type: Any[]
steps: steps:
- id: DP3_GenericStep - id: DP3_GenericStep
in: in:
- id: parameters_input - id: steps
source: parameters_input source: steps
- id: output_files - id: output_files
default: ["instrumentmodel"] default: ["instrumentmodel"]
...@@ -182,7 +182,7 @@ steps: ...@@ -182,7 +182,7 @@ steps:
- id: maxiter - id: maxiter
source: maxiter source: maxiter
out: out:
- parameters_out - augmented_steps
run: ../steps/DP3.GenericStep.cwl run: ../steps/DP3.GenericStep.cwl
requirements: requirements:
- class: StepInputExpressionRequirement - class: StepInputExpressionRequirement
......
...@@ -8,14 +8,14 @@ requirements: ...@@ -8,14 +8,14 @@ requirements:
- class: InlineJavascriptRequirement - class: InlineJavascriptRequirement
inputs: inputs:
- id: parameters_input - id: steps
type: Any[] type: Any[]
- id: parameters - id: parameters
type: Any? type: Any?
outputs: outputs:
- id: parameters_out - id: augmented_steps
type: Any[] type: Any[]
expression: |- expression: |-
${ ${
...@@ -36,9 +36,9 @@ expression: |- ...@@ -36,9 +36,9 @@ expression: |-
delete inputs.parameters.step_type; delete inputs.parameters.step_type;
delete inputs.parameters.step_id; delete inputs.parameters.step_id;
delete inputs.parameters.parameters_input; delete inputs.parameters.steps;
delete inputs.parameters.parameters; delete inputs.parameters.parameters;
delete inputs.parameters.parameters_input; delete inputs.parameters.steps;
var new_step = {'step_type': step_type, var new_step = {'step_type': step_type,
...@@ -47,7 +47,7 @@ expression: |- ...@@ -47,7 +47,7 @@ expression: |-
'output_files': output_files}; 'output_files': output_files};
var in_parameters = inputs.parameters_input; var in_parameters = inputs.steps;
// Checks if the step_id is duplicate if so raised an exception // Checks if the step_id is duplicate if so raised an exception
var step_ids = [] var step_ids = []
...@@ -59,5 +59,5 @@ expression: |- ...@@ -59,5 +59,5 @@ expression: |-
var out_parameters = in_parameters == null ? [new_step] : in_parameters.concat(new_step) var out_parameters = in_parameters == null ? [new_step] : in_parameters.concat(new_step)
return {'parameters_out': out_parameters}; return {'augmented_steps': out_parameters};
} }
...@@ -18,7 +18,7 @@ arguments: ...@@ -18,7 +18,7 @@ arguments:
true = True true = True
false = False false = False
null = None null = None
steps_list = $(inputs.parameters_input) steps_list = $(inputs.steps)
steps_id_list = list(map(lambda item: item['step_id'], steps_list)) steps_id_list = list(map(lambda item: item['step_id'], steps_list))
for step in steps_list: for step in steps_list:
...@@ -50,15 +50,15 @@ arguments: ...@@ -50,15 +50,15 @@ arguments:
last_step_line = 'steps=[%s]' % ', '.join(steps_id_list) last_step_line = 'steps=[%s]' % ', '.join(steps_id_list)
print(last_step_line) print(last_step_line)
inputs: inputs:
- id: parameters_input - id: steps
type: Any[]? type: Any[]?
outputs: outputs:
- id: output_parset - id: parset
doc: Parset output file doc: Parset output file
type: File type: File
outputBinding: outputBinding:
glob: output_parset glob: parset
- id: input_files - id: input_files
doc: additional input files doc: additional input files
type: File[] type: File[]
...@@ -66,8 +66,8 @@ outputs: ...@@ -66,8 +66,8 @@ outputs:
outputEval: |- outputEval: |-
${ ${
var outfiles = [] var outfiles = []
for(var step in inputs.parameters_input){ for(var step in inputs.steps){
step = inputs.parameters_input[step] step = inputs.steps[step]
for(var parameter in step['parameters']){ for(var parameter in step['parameters']){
parameter = step['parameters'][parameter] parameter = step['parameters'][parameter]
...@@ -85,8 +85,8 @@ outputs: ...@@ -85,8 +85,8 @@ outputs:
outputEval: | outputEval: |
${ ${
var outdirs = [] var outdirs = []
for(var step in inputs.parameters_input){ for(var step in inputs.steps){
step = inputs.parameters_input[step] step = inputs.steps[step]
for(var parameter in step['parameters']){ for(var parameter in step['parameters']){
parameter = step['parameters'][parameter] parameter = step['parameters'][parameter]
if (parameter != null && parameter.class=='Directory'){ if (parameter != null && parameter.class=='Directory'){
...@@ -104,8 +104,8 @@ outputs: ...@@ -104,8 +104,8 @@ outputs:
outputEval: | outputEval: |
${ ${
var out_names = {} var out_names = {}
for(var step_idx in inputs.parameters_input){ for(var step_idx in inputs.steps){
var step = inputs.parameters_input[step_idx] var step = inputs.steps[step_idx]
var step_id = step['step_id'] var step_id = step['step_id']
var step_dirs = {} var step_dirs = {}
if(!step.hasOwnProperty("output_files")) continue; if(!step.hasOwnProperty("output_files")) continue;
...@@ -129,8 +129,8 @@ outputs: ...@@ -129,8 +129,8 @@ outputs:
outputEval: |- outputEval: |-
${ ${
var out_names = {} var out_names = {}
for(var step_idx in inputs.parameters_input){ for(var step_idx in inputs.steps){
var step = inputs.parameters_input[step_idx] var step = inputs.steps[step_idx]
var step_id = step['step_id'] var step_id = step['step_id']
var step_dirs = {} var step_dirs = {}
if(!step.hasOwnProperty("output_directories")) continue; if(!step.hasOwnProperty("output_directories")) continue;
...@@ -145,4 +145,4 @@ outputs: ...@@ -145,4 +145,4 @@ outputs:
return out_names return out_names
} }
stdout: stdout:
output_parset parset
...@@ -5,7 +5,7 @@ cwlVersion: v1.0 ...@@ -5,7 +5,7 @@ cwlVersion: v1.0
id: preflag_step_generator id: preflag_step_generator
inputs: inputs:
- id: input_parset - id: steps
type: Any[]? type: Any[]?
default: [] default: []
- id: step_name - id: step_name
...@@ -169,9 +169,9 @@ inputs: ...@@ -169,9 +169,9 @@ inputs:
type: float type: float
doc: Correlation data with imaginary complex part > imagmax will match. doc: Correlation data with imaginary complex part > imagmax will match.
outputs: outputs:
- id: parameters_out - id: augmented_steps
outputSource: outputSource:
- DP3_GenericStep/parameters_out - DP3_GenericStep/augmented_steps
type: Any[] type: Any[]
steps: steps:
...@@ -181,8 +181,8 @@ steps: ...@@ -181,8 +181,8 @@ steps:
default: 'preflagger' default: 'preflagger'
- id: step_id - id: step_id
source: step_name source: step_name
- id: parameters_input - id: steps
source: input_parset source: steps
- id: parameters - id: parameters
valueFrom: $(inputs) valueFrom: $(inputs)
- id: count.save - id: count.save
...@@ -238,7 +238,7 @@ steps: ...@@ -238,7 +238,7 @@ steps:
- id: imagmax - id: imagmax
source: imagmax source: imagmax
out: out:
- parameters_out - augmented_steps
run: ../steps/DP3.GenericStep.cwl run: ../steps/DP3.GenericStep.cwl
requirements: requirements:
......
class: ExpressionTool class: ExpressionTool
cwlVersion: v1.0 cwlVersion: v1.0
id: parsetselector id: selector
inputs: inputs:
- id: select_a - id: select_a
type: boolean type: boolean
doc: 'if true selects parset_a, files_a if false selects parset_b files_b' doc: 'if true selects a_steps if false selects b_steps'
- id: a_arguments - id: a_steps
type: Any[] type: Any[]
default: [] default: []
- id: b_arguments - id: b_steps
type: Any[] type: Any[]
default: [] default: []
outputs: outputs:
- id: output_arguments - id: selected_steps
type: Any type: Any
expression: | expression: |
$( $(
{'output_arguments': inputs.selector ? inputs.a_arguments : inputs.b_arguments} {'selected_steps': inputs.selector ? inputs.a_steps : inputs.b_steps}
) )
label: ParsetSelector label: Selector
requirements: requirements:
- class: InlineJavascriptRequirement - class: InlineJavascriptRequirement
...@@ -7,16 +7,16 @@ $namespaces: ...@@ -7,16 +7,16 @@ $namespaces:
inputs: inputs:
- id: baselines_to_flag - id: baselines_to_flag
type: 'string[]' type: 'string[]'
'sbg:x': 707.7924194335938 'sbg:x': 732.2234497070312
'sbg:y': -366.86871337890625 'sbg:y': 79.11939239501953
- id: elevation_to_flag - id: elevation_to_flag
type: string type: string
'sbg:x': 847 'sbg:x': 815.8416137695312
'sbg:y': -501.7469482421875 'sbg:y': -281.40777587890625
- id: min_amplitude_to_flag - id: min_amplitude_to_flag
type: float type: float
'sbg:x': 1129.3828125 'sbg:x': 964.3058471679688
'sbg:y': 338.9372863769531 'sbg:y': 191.110595703125
- id: memoryperc - id: memoryperc
type: int type: int
'sbg:x': 136.78256225585938 'sbg:x': 136.78256225585938
...@@ -31,8 +31,8 @@ inputs: ...@@ -31,8 +31,8 @@ inputs:
'sbg:y': -298.45196533203125 'sbg:y': -298.45196533203125
- id: msin - id: msin
type: Directory? type: Directory?
'sbg:x': 2095.969482421875 'sbg:x': 2129.6337890625
'sbg:y': 563.7855224609375 'sbg:y': 149.5590362548828
outputs: outputs:
- id: msout - id: msout
outputSource: outputSource:
...@@ -49,76 +49,80 @@ outputs: ...@@ -49,76 +49,80 @@ outputs:
steps: steps:
- id: flagbaseline - id: flagbaseline
in: in:
- id: input_parset - id: steps
source: source:
- process_raw_data_select/output_arguments - process_raw_data_select/selected_steps
- id: step_name - id: step_name
default: flagbaseline default: flagbaseline
- id: baseline - id: baseline
source: source:
- baselines_to_flag - baselines_to_flag
out: out:
- id: parameters_out - id: augmented_steps
run: ../steps/DP3.PreflaggerStepGenerator.cwl run: ../steps/DP3.PreflaggerStepGenerator.cwl
'sbg:x': 1160.802978515625 'sbg:x': 955.2450561523438
'sbg:y': -95.15213775634766 'sbg:y': -75.71149444580078
- id: flagelev - id: flagelev
in: in:
- id: input_parset - id: steps
source: source:
- flagbaseline/parameters_out - flagbaseline/augmented_steps
- id: step_name - id: step_name
default: flagelev default: flagelev
- id: elevation - id: elevation
source: elevation_to_flag source: elevation_to_flag
out: out:
- id: parameters_out - id: augmented_steps
run: ../steps/DP3.PreflaggerStepGenerator.cwl run: ../steps/DP3.PreflaggerStepGenerator.cwl
'sbg:x': 1459.2421875 'sbg:x': 1187.4771728515625
'sbg:y': -83.970458984375 'sbg:y': -83
- id: process_raw_data_select - id: process_raw_data_select
in: in:
- id: select_a - id: select_a
source: raw_data source: raw_data
- id: a_arguments - id: a_steps
source: source:
- aoflag/parameters_out - aoflag/augmented_steps
- id: b_steps
default: []
out: out:
- id: output_arguments - id: selected_steps
run: ../steps/DP3.ParsetSelector.cwl run: ../steps/DP3.Selector.cwl
label: ParsetSelector label: Selector
'sbg:x': 621.4892578125 'sbg:x': 621.4892578125
'sbg:y': -71.31844329833984 'sbg:y': -71.31844329833984
- id: flagamp - id: flagamp
in: in:
- id: input_parset - id: steps
source: source:
- flagelev/parameters_out - flagelev/augmented_steps
- id: step_name - id: step_name
default: flagamp default: flagamp
- id: amplmin - id: amplmin
source: min_amplitude_to_flag source: min_amplitude_to_flag
out: out:
- id: parameters_out - id: augmented_steps
run: ../steps/DP3.PreflaggerStepGenerator.cwl run: ../steps/DP3.PreflaggerStepGenerator.cwl
'sbg:x': 1659.302001953125 'sbg:x': 1385.993408203125
'sbg:y': -23 'sbg:y': -42.28850555419922
- id: flagedge - id: flagedge
in: in:
- id: step_name - id: step_name
default: flagedge default: flagedge
- id: steps
default: []
- id: chan - id: chan
default: '[0..nchan/32-1,31*nchan/32..nchan-1]' default: '[0..nchan/32-1,31*nchan/32..nchan-1]'
out: out:
- id: parameters_out - id: augmented_steps
run: ../steps/DP3.PreflaggerStepGenerator.cwl run: ../steps/DP3.PreflaggerStepGenerator.cwl
'sbg:x': 53.59375762939453 'sbg:x': 122.25408935546875
'sbg:y': -119.96077728271484 'sbg:y': -54.06163024902344
- id: aoflag - id: aoflag
in: in:
- id: parameters_input - id: steps
source: source:
- flagedge/parameters_out - flagedge/augmented_steps
- id: step_name - id: step_name
default: aoflag default: aoflag
- id: memoryperc - id: memoryperc
...@@ -126,54 +130,54 @@ steps: ...@@ -126,54 +130,54 @@ steps:
- id: keepstatistics - id: keepstatistics
default: false default: false
out: out:
- id: parameters_out - id: augmented_steps
run: ../steps/DP3.AOFlaggerStepGenerator.cwl run: ../steps/DP3.AOFlaggerStepGenerator.cwl
'sbg:x': 357.934326171875 'sbg:x': 369.9876708984375
'sbg:y': -129.337890625 'sbg:y': -38.086280822753906
- id: demix_select - id: demix_select
in: in:
- id: select_a - id: select_a
source: demix source: demix
- id: a_arguments - id: a_steps
source: source:
- demixstepgenerator/parameters_out - demixstepgenerator/augmented_steps
- id: b_arguments - id: b_steps
source: source:
- flagamp/parameters_out - flagamp/augmented_steps
out: out:
- id: output_arguments - id: selected_steps
run: ../steps/DP3.ParsetSelector.cwl run: ../steps/DP3.Selector.cwl
label: demix? label: demix?
'sbg:x': 1985.5047607421875 'sbg:x': 1985.5047607421875
'sbg:y': -44.651588439941406 'sbg:y': -44.651588439941406
- id: demixstepgenerator - id: demixstepgenerator
in: in:
- id: parameters_input - id: steps
source: source:
- flagamp/parameters_out - flagamp/augmented_steps
out: out:
- id: parameters_out - id: augmented_steps
run: ../steps/DP3.DemixerStepGenerator.cwl run: ../steps/DP3.DemixerStepGenerator.cwl
'sbg:x': 1828.623046875 'sbg:x': 1676.6593017578125
'sbg:y': 156.3474578857422 'sbg:y': 90.7158203125
- id: parsetgenerator - id: parsetgenerator
in: in:
- id: parameters_input - id: steps
source: source:
- demix_select/output_arguments - demix_select/selected_steps
out: out:
- id: output_parset - id: parset
- id: input_files - id: input_files
- id: input_directories - id: input_directories
- id: output_file_names - id: output_file_names
- id: output_directory_names - id: output_directory_names
run: ../steps/DP3.ParsetGenerator.cwl run: ../steps/DP3.ParsetGenerator.cwl
'sbg:x': 2228.349365234375 'sbg:x': 2228
'sbg:y': -53.74734115600586 'sbg:y': -40.012325286865234
- id: dppp - id: dppp
in: in:
- id: parset - id: parset
source: parsetgenerator/output_parset source: parsetgenerator/parset
- id: msin - id: msin
source: msin source: msin
- id: msout_name - id: msout_name
...@@ -215,3 +219,4 @@ requirements: ...@@ -215,3 +219,4 @@ requirements:
- class: SubworkflowFeatureRequirement - class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement - class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement - class: InlineJavascriptRequirement
{ {
"msin": { "msin": {
"class":"File", "class": "Directory",
"path": "/data/L570745_SB001_uv_first10.MS" "path": "/data/L570745_SB001_uv_first10.MS"
} }
} }
File moved
...@@ -20,27 +20,27 @@ steps: ...@@ -20,27 +20,27 @@ steps:
- id: aoflagger_step_generator - id: aoflagger_step_generator
in: [] in: []
out: out:
- id: parameters_out - id: augmented_steps
run: ../steps/DP3.AOFlaggerStepGenerator.cwl run: ../steps/DP3.AOFlaggerStepGenerator.cwl
'sbg:x': -1357.640625 'sbg:x': -1357.640625
'sbg:y': -729.5 'sbg:y': -729.5
- id: average_step_generator - id: average_step_generator
in: in:
- id: input_parset - id: steps
source: source:
- aoflagger_step_generator/parameters_out - aoflagger_step_generator/augmented_steps
out: out:
- id: parameters_out - id: augmented_steps
run: ../steps/DP3.AveragerStepGenerator.cwl run: ../steps/DP3.AveragerStepGenerator.cwl
'sbg:x': -1125 'sbg:x': -1125
'sbg:y': -729 'sbg:y': -729
- id: parset_generator - id: parset_generator
in: in:
- id: parameters_input - id: steps
source: source:
- average_step_generator/parameters_out - average_step_generator/augmented_steps
out: out:
- id: output_parset - id: parset
- id: input_files - id: input_files
- id: input_directories - id: input_directories
- id: output_file_names - id: output_file_names
...@@ -51,7 +51,7 @@ steps: ...@@ -51,7 +51,7 @@ steps:
- id: dppp - id: dppp
in: in:
- id: parset - id: parset
source: parset_generator/output_parset source: parset_generator/parset
- id: msin - id: msin
source: msin source: msin
- id: secondary_files - id: secondary_files
......
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