Mark Polster

empty cell_id column in airr file from 10x Genomics data

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Hey guys! I am running TRUST4 on 10xGenomics RNAseq data. Especially, we make use of the AIRR file for our post-processing analysis. For a QC protocol, we require the `cell_ids`,...

After adding the single-cell dataset, the respective README part is added with this PR

Potential bug when using paired-end files

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Hi, I found some weird behaviour when running paired-end data. To test some stuff, I created some simulated datasets where I know all the parameters like repertoire size, size of...

Fastp sc

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This pr adds the fastp module to the raw single cell based subworkflow.

bump cellranger version

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Bump cellranger vdj version from 7.1.0 to 8.0.0.

include MiXCR toolkit in nf-core/airrflow

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This PR includes MiXCR preprocessing in the nf-core/airrflow pipelines. It allows to integrate MiXCR preprocessing in the the pipeline, finishing with immcantation postprocessing. MiXCR postprocessing can be performed additionnally as...

### Description of feature RNA-seq based HLA typing

topic channels blog post

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blogpost to describe how to adopt topic channels for nf-core modules. Includes description of topic channels and tutorial to adopt a module @netlify /blog/2025/version_topics

### Is there an existing module for this? - [x] I have searched for the existing module ### Is there an open PR for this? - [x] I have searched...