Redmar van den Berg

Using modules, you can import rules without directly using them. I made an example of several modules that can be run independently, or as part of a bigger workflow. See...

@rcaneill I like to tests my pipelines using singularity and [pytest-workflow](https://pytest-workflow.readthedocs.io/en/stable/#writing-tests-with-pytest-workflow), you can see my example project [here](https://github.com/Redmar-van-den-Berg/snakemake-project). It includes caching for both `conda` and `singularity`, which makes the tests...

Does this bug still occur if you add the script as an `input` dependency, and use the `srcdir` keyword?

The documentation for the latest version of Snakemake shows how to use [modules](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#modules).

I run into the same issue with snakemake 7.8.5, are there any plans to address this issue?

You mean when the shell section refers to `{input.bam}`, while there is no `bam` file defined in the `input` section of the rule? It might be better to check that...

We did run our capture protocol on one of the GIAB trio's, so we can share that data with you in the new year.

This is the best sequencing batch we have for the GIAB trio with our protocol: [mother](https://barmsijs.lumc.nl/rrvandenberg/for_hifiasm/GM24143_0_1x_full_opt.dedup.fastq.gz) [father](https://barmsijs.lumc.nl/rrvandenberg/for_hifiasm/GM24149_0_1x_full_opt.dedup.fastq.gz) [child](https://barmsijs.lumc.nl/rrvandenberg/for_hifiasm/GM24385_0_1x_full_opt.dedup.fastq.gz)

Is there any news on this front? I like to test my pipelines with some data for chrM, so it would be great to be able to use Nirvana with...

This is not necessarily the case. For example, it is possible that all tests pass, but only the exit code is non-zero. This can happen easily with Snakemake, which generates...