A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Thanks - still having challenging issues with this pipeline not completing. After renaming all the conditions to have only letters and numbers and one single "_" before "REP1", 2, 3, I had a new error:

`ERROR ~ Error executing process &gt; 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU (1)'`
...
`Warning message:`  
  `In DESeqDataSet(rse, design, ignoreRank = TRUE) :`   
  `some variables in design formula are characters, converting to factors`
  `Error in nbinomLRT(x, reduced = reducedModelMatrix, full = fullModelMatrix)`  
    `less than one degree of freedom, perhaps full and reduced models are not in the correct order`   
  `Calls: lapply ... tryCatch -&gt; tryCatchList -&gt; tryCatchOne -&gt; &lt;Anonymous&gt;`    
  `Execution halted`                                                    
  `INFO:    Cleaning up image...`       

Any suggestions on how best to format the samplesheets would be appreciated. Also, carrying over already mapped data from the rnaseq pipeline (e.g. in transcriptome bam) seems to fail. Maybe same issue of naming?

I don't think I have seen that one.  Maybe something missing in your contrast sheet?  Do you want to post your contrast sheet and the sample sheet?