Pipeline releases
Below is a list of the pipeline releases that should be used at QBiC for the analysis. Unless a release has a bug that makes it impossible to work with your data, please use this fixed releases. These versions will be revised periodically and tested in our infrastructure before update.
Pipeline releases to be used at QBiC
| Analysis type | Pipeline | Use version |
|---|---|---|
| RNAseq | nf-core/rnaseq | 1.4.2 |
| RNAseq DE analysis | qbic-pipelines/rnadeseq | 2.1 |
| WGS / WES | nf-core/sarek | 3.1.2 |
| HLAtyping | nf-core/hlatyping | 1.2.0 |
| 16S amplicon | nf-core/ampliseq | 2.1.1 |
| Shotgun metagenomics | nf-core/mag | 2.1.1 |
| BCR / TCR repseq | nf-core/airrflow | 2.4.0 |
| CAGEseq | nf-core/cageseq | 1.0.2 |
| MHC immunopeptidomics | nf-core/mhcquant | 2.3.1 |
| ATACseq | nf-core/atacseq | 1.2.2 |
| Chipseq | nf-core/chipseq | 1.2.2 |
| Epitope prediction | nf-core/epitopeprediction | 2.0.0 |
| Bacterial assembly | nf-core/bacass | 2.0.0 |
| RNA fusion | nf-core/rnafusion | 1.2.0 |
| scRNAseq cellranger | qbic-pipelines/cellranger | 1.0.1 |
| BAM/CRAM to Fastq | qbic-pipelines/bamtofastq | 1.2.0 |