Filipe G. Vieira

**Describe the bug** **To Reproduce** Steps to reproduce the behavior: 1. Upload any `json` to megaqc 2. See error: ``` Traceback (most recent call last): File "lib/python3.11/site-packages/megaqc/scheduler.py", line 60, in...

**Describe the bug** I am trying to plot the FastQC module multiple times (like [here](https://multiqc.info/docs/reports/customisation/#running-modules-multiple-times)) but, even though all looks good in the `MultiQC` report, only the last data seems...

**Describe the bug** `python 3.12` is not supported. **To Reproduce** Steps to reproduce the behavior: 1. Run megaqc with command: `initdb` 2. See error ``` [...] import imp ModuleNotFoundError: No...

[FEATURE REQUEST]: remove prefix to sequence names

3

*Is this a feature request for FCS-adaptor or FCS-GX?* Yes *Describe the problem you'd like to be solved* At the moment, the output of FCS add a prefix to the...

fix: checkpoints inside modules are overwritten

1

### Description When including two modules with checkpoints (or the same module twice with different prefixes), only the checkpoint of the last loaded module is used. In the example here,...

Bind current working directory to container

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**Is your feature request related to a problem? Please describe.** A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] When using a container,...

feat: Updated description and added mamba

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### Description Add `mamba` to the install requirements since, even though it is not required, it is recommended to use by the developers. Updating python version description. Bioconda recipe still...

Error when using wrappers and `use rule as`

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**Snakemake version** `v8.10.8` **Describe the bug** The use of `wrapper` with `use rule ... as ... with` is incompatible. **Logs** Error message: ``` SyntaxError in file /home/lnc113/TEST/Snakefile, line 6: Unexpected...

Incomplete DAG with checkpoints

3

**Snakemake version** `v8.10.7` **Describe the bug** DAG is incomplete when there are checkpoints, since it only plots the DAG for the rules upstream of the checkpoint. **Minimal example** On test...

**Snakemake version** v7.32.4 **Describe the bug** I am trying to set resources based on input file size as: ``` resources: runtime = lambda w, attempt, input: input.size_mb * 7 *...