Hi all,
I think providing CWL workflows in debian is a great idea. However, I
On 11.08.2017 17:57, Steffen Möller wrote:
> I had an exchange with Stian yesterday about what CWL workflow of his
> database he would propose to use as an experience-gathering example. He
> proposed the GATK workflow by Farah Zaib Khan et al. for being good to
> cite about workflows and reproducibility.
have another use case in mind: We know that bioinformatics is mostly
converting from one file format to the other. Given the EDAM annotation
which has already been added to various packages, one can propose the
user tools to do the conversion. If we had CWL tool descriptions, one
would be able to tell the user how to call the tool to achieve the
desired effect. With a fitting workflow one would be able to do the
conversion automatically.
The combination of CWL + EDAM provides some very nice synergistic
effects. However, the lack of annotated tools might make achieving the
functionality, as stated above, a big effort. Neither bio.tools, nor the
CWL repo contain enough entries to really be useful. Borrowing from the
other discussion, Appstream might be a way to let the author of a tool
provide this metadata, relieving the packagers of some work.
Hope this text was somewhat comprehensible; My thoughts on this are
still in a rough state.
Best,
Fabian