lufpa / tm3seq-pipeline Goto Github PK

Before running the pipeline, add a check point to verify whether the samples have been found, if not, abort here with a clear msg. It may be common that users forget to modify sample id in the config.defaults.yml file.

Add some specifications on how to provide the genome. E.g. provide the fasta file and indexes will be created, or allow pre-indexed files for STAR.

Lance, some users are interested in using PE reads with this pipeline. I double checked the rules and from the trimming step it is working only on SE. Could we update this to make it flexible?