Nico Trummer

Attempt solving #155

7

Tries to solve the problem of CIRIquant not being able to access the GTF file by staging it to the working directory

Documentation can be found [here](https://github.com/Christina-hshi/psirc?tab=readme-ov-file#general-usages) ```[tasklist] ### Tasks - [x] Set up environment - [ ] Implement process ```

### Description of feature [Kallisto module docs](https://multiqc.info/modules/kallisto/)

Documentation can be found [here](https://github.com/tofazzalh/circRNAFull) The function [`extract_sequence`](https://github.com/tofazzalh/circRNAFull?tab=readme-ov-file#reconstruction-of-full-length-circrna-sequences) appears to be most relevant ```[tasklist] ### Tasks - [ ] Make sure the necessary outputs from `STAR` are available - [...

Documentation can be found [here](https://ciri-cookbook.readthedocs.io/en/latest/CIRI-full.html). ```[tasklist] ### Tasks - [ ] Make sure outputs of `BWA` are available - [ ] Implement CIRI - [ ] Implement CIRI-AS - [...

Documentation can be found [here](https://github.com/cbbzhang/JCcirc). Implement options for creating contig files: ```[tasklist] ### Tasks - [ ] Trinity - [ ] SPAdes - [ ] SOAPdenovo-Trans - [ ] Add...

### Description of feature Perform a parallel execution of `CIRCRNA_DISCOVERY` using polyA-enriched data to investigate the tendency of tools to find circRNAs in datasets where there should not be any....

### Description of feature As described in [this paper](https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad093/7221568)

Fix solo bug with large batches

2

Hello everyone, this is my first time contributing here, so let me know if I got something wrong with the way I approached this. I have a very large batch...

### Description of feature Docs can be found [here](https://github.com/vpc-ccg/circminer)