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(define-module (gn packages cwl)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix download)
#:use-module (guix packages)
#:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages node)
(define-public cwl-runner
(package
(name "cwl-runner")
(version "1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cwl_runner" version))
(sha256
(base32
"0011am2xqwchysdznayrmwhg4bfjl4wlq6m4k20z1m7gccyzjgw0"))))
(build-system python-build-system)
(propagated-inputs
`(("cwltool" ,cwltool)))
(home-page
"https://github.com/common-workflow-language/common-workflow-language")
(synopsis "Common workflow language reference implementation")
(description
"Common workflow language alternate entry point to allow cwl-runner
script as an implementation-agnostic script interpreter.")
(license license:asl2.0)))
;; python-toil tightly integrates with cwltool using it as a library. So,
;; create a library version of cwltool where inputs become propagated inputs.
(define-public python-cwltool
(package
(inherit cwltool)
(name "python-cwltool")
(inputs
(list node))
(propagated-inputs
(modify-inputs (package-inputs cwltool)
(delete "node")))))
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