-
We need to review what https://nf-co.re/sarek can do to determine:
- if it could be used as is
- if it could be used with modifications
- if we'd rather extract and replicate some functionality h…
-
## Input specifications
To skip the qc and assembly step we can provide the assemblies and reads used to generate the assemblies in a CSV file together with a CSV file specifying the reads.
The asse…
-
## nf-core
nf-core produces pipelines with gold standard tools for various analyses.
- Workflow manager using `nextflow` language.
- Compatible with SLURM
- Uses Docker, Singularity and conda t…
-
nf-core offers a lot of best practices and associated tooling for developing new pipelines, which we've mostly ignored in the current pipeline. I would like to rework the pipeline to be compatible wit…
-
There is a few problems / hurdles / efficiency issues using `nf-core` right now. Let's use this issue to list them and discuss.
- [ ] `git-remote` and `branch` in commands to target `nf-scil`
- [ …
-
### Have you checked the docs?
- [X] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [X] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules)
### …
-
Hi, I've noticed you are using Baysor in your pipeline. Are there any plans on making it an official nf-core module (or set of modules for it)?
There is an opened issue in the nf-core/modules repo:…
-
> [!WARNING]
> Please open PRs against the `batch_update_staging` branch. Then we can have small, easy to review, atomic PRs but also merge all batch updates to the modules repo in one go.
```[tas…
-
**Description**
I am currently working on adding `Dysgu` as a new module in nf-core/modules, with the aim of later incorporating it into the nf-core/sarek pipeline for Structural Variant (SV) calling…
-
### Description of feature
The following methods look interesting:
```[tasklist]
### Tasks
- [ ] https://github.com/nf-core/scdownstream/issues/21
- [ ] https://github.com/nf-core/scdownstream/issue…