janis

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Was reading the docs today while testing some WDL workflow, when I noticed a formatting that appeared to be incorrect. I think the `1. Step based:` is highlighted due to...

kinow

Missing .gitmodules?

2

Hi, I see `.gitmodules` was removed in [this commit](83a51c20d014184dfaac8694d4ce23e5bbb8a604), but the directories `janis-core` and `janis-assistant` were kept, as well as the `updatesubmodules.sh` script. Should these be removed as well? Cheers...

kinow

Several warnings when downloading data for Tutorial 1

1

When executing `wget` or `curl` with `wget -q -O- "https://github.com/PMCC-BioinformaticsCore/janis-workshops/raw/master/janis-data.tar" | tar -x` (removed the `z`, see #51 for more) the file is successfully downloaded and uncompressed. However, there are...

kinow

The `tools/alighment.py` file is first created in the [tutorial 1](https://janis.readthedocs.io/en/latest/tutorials/tutorial1.html). ```py # File: tools/alignment.py from janis_core import WorkflowBuilder, String from janis_bioinformatics.data_types import FastqGzPairedEnd, FastaWithDict from janis_bioinformatics.tools.bwa import BwaMemLatest from janis_bioinformatics.tools.samtools...

kinow

Hello, I learned about Janis yesterday after an e-mail sent to the AU/NZ RSE mailing list. Really interesting project, and the code is super organized, and the docs are beyond...

kinow

documentation on mapping WDL concepts to CWL concepts

1

FYI https://github.com/dnanexus/dxCompiler/blob/main/doc/CWL_v1.2.0_to_WDL_v1.md Where can I learn more about the status of Janis importing WDL?

mr-c

An issue to keep tabs on documentation, and which things need to be documented: #### General - [ ] Engine comparison - Call-caching - Debugging - Logging - Execution environment...

illusional

FYI @junyk I believe this is because a `SystemExit` error is raised (by calling `sys.exit`) if the workflow / tool fails to run: https://github.com/PMCC-BioinformaticsCore/janis-assistant/blob/fbcefc665a9a23073830acb8f87cc41ea58bcf8f/janis_assistant/management/workflowmanager.py#L595-L598. These need to [be caught separately](https://www.tutorialspoint.com/How-to-catch-SystemExit-Exception-in-Python).

illusional

With the amount of ad-hoc scripts, and increasing janis functionality, it's useful to group a number of developer-focused functionality into a little toolkit. For example - Generating tool wrappers -...

illusional

documentation: subworkflows

9

Hi, Would it be possible to add a quick comment on how to use subworkflows? Do I just add them as in a "master" workflow? Thanks M

matthdsm