recipe bioconductor-rcwl

An R interface to the Common Workflow Language



GPL-2 | file LICENSE



The Common Workflow Language (CWL) is an open standard for development of data analysis workflows that is portable and scalable across different tools and working environments. Rcwl provides a simple way to wrap command line tools and build CWL data analysis pipelines programmatically within R. It increases the ease of usage, development, and maintenance of CWL pipelines.

package bioconductor-rcwl

(downloads) docker_bioconductor-rcwl



depends bioconductor-basilisk:


depends bioconductor-biocparallel:


depends bioconductor-s4vectors:


depends r-base:


depends r-batchtools:

depends r-codetools:

depends r-diagrammer:

depends r-r.utils:

depends r-shiny:

depends r-yaml:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-rcwl

and update with::

   mamba update bioconductor-rcwl

To create a new environment, run:

mamba create --name myenvname bioconductor-rcwl

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-rcwl/tags`_ for valid values for ``<tag>``)

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