Oliver Ziff

Thanks @blueskypie but those arguments are already set and the row ordering is lost with `row_split = factor(topVar$database, levels = c(1,2))`

i ran the RNAseq pipeline on 576 fastq files and the slurm submission has also failed on the multiqc process with the same error: `sbatch: error: Batch job submission failed:...

Thanks @drpatelh! Yes this approach seems the best way forwards as `infer_experiment.py` needs an aligned bam file. Although from your list i cant see STAR so one possibility is to...

Hi @ChiaraF32 As many of the processes require the correct strandedness, unfortunately, you need to re-run the pipeline with the correct strandedness in the samplesheet.csv. You can sometimes see in...

Yes @lincoln-harris, the instructions say optional but the help `-h` states required: ``` --cosmicdb TEXT path to cosmic db file (.tsv) [required] ``` Please could you advise which cosmic tsv...

I have this same query: How do we compare groups of biological replicates? In the [vignette](https://bioconductor.org/packages/devel/bioc/vignettes/DEP/inst/doc/DEP.html#differential-enrichment-analysis), there is only an example of how to compare groups of technical replicates (Ubi4_vs_Ubi6,...

Adding `--DROP_MISSING_CONTIGS TRUE` to my config gets around the missing contigs error in `GATK4_BEDTOINTERVALLIST`: ``` process { withName: 'NFCORE_RNAVAR:RNAVAR:GATK4_BEDTOINTERVALLIST' { ext.args = '--DROP_MISSING_CONTIGS TRUE' } } ```