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utility to replace CWL expressions with either ExpressionTools or CommandLineTools #5

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merged 37 commits into from Jan 10, 2020
Merged

utility to replace CWL expressions with either ExpressionTools or CommandLineTools #5

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32aabf3
add v1.1 parser
mr-c Jul 4, 2019
90cfda0
regen v1.0
mr-c Jul 4, 2019
e0e4cd8
add script to replace ExpressionTools with CommandLineTools
mr-c Jul 5, 2019
7e43c72
nicer output and some comments
mr-c Jul 6, 2019
fa8cbe3
regen v1.1
mr-c Jul 6, 2019
aa37e6f
oops, shouldn't have an InlineJavascriptRequirement!
mr-c Jul 6, 2019
f0c6903
convert etools inplace in workflows
mr-c Jul 6, 2019
bfe8a82
replace CWL expressions with separate steps
mr-c Jul 6, 2019
8e3716c
support expressionLib
mr-c Jul 6, 2019
1750114
expression in Workflow.inputs.{format,secondaryFiles}
mr-c Jul 6, 2019
babe3d2
expr in Workflow level ResourceReqs and IWDRs
mr-c Jul 6, 2019
c8ae681
Workflow.reqs.EnvVarRequirement
mr-c Jul 7, 2019
b231428
start to support CWL expr in $(…) format
mr-c Jul 7, 2019
e63b2c2
process level reqs
mr-c Jul 7, 2019
aa247ee
add Workflow.steps[](CommandLineTool).arguments; remove Workflow.inpu…
mr-c Jul 8, 2019
8b54c3e
linking inputs for CLT.args; add CLT.{stdout,stderr}
mr-c Jul 8, 2019
f50b19b
CommandLineTool.inputs{}.inputBinding.valueFrom
mr-c Jul 8, 2019
460206d
CommandLineTool.outputs[].outputBinding.glob
mr-c Jul 8, 2019
17228f9
CommandLineTool.outputs[].outputBinding.outputEval
mr-c Jul 8, 2019
dfa47cb
170 tests pass, 27 fail
mr-c Nov 19, 2019
854039c
thank you @lgtm-com
mr-c Nov 19, 2019
05e77a4
fix a type
mr-c Nov 19, 2019
3be2a53
187 tests passed, 10 failures
mr-c Nov 20, 2019
274b2cf
convert standalone CommandLineTools to be Workflows, if necessary
mr-c Nov 20, 2019
16ab2f1
improve target type search
mr-c Nov 20, 2019
c58f23d
191 tests passed, 6 failures
mr-c Nov 20, 2019
5f212b6
skip inputBinding.valueFrom and arguments[n].valueFrom for now
mr-c Nov 20, 2019
b2771a6
All tests passed
mr-c Nov 20, 2019
f1c8816
typo
mr-c Nov 20, 2019
e174a22
resume refactoring CWL expressions that use the $() syntax
mr-c Nov 20, 2019
aa6fad9
more refactoring to support $() CWL expressions
mr-c Nov 21, 2019
60229bf
handle stdout
mr-c Nov 21, 2019
dcb3e1b
remove some CWL expression false positives
mr-c Nov 21, 2019
cb7425a
Improve InitialWorkDirRequirement
mr-c Nov 21, 2019
2e5b22a
195 tests passed, 2 failures
mr-c Nov 21, 2019
906827d
mypy inspired cleanups & fixes
mr-c Nov 21, 2019
12c7b52
misc
mr-c Jan 8, 2020
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