Galaxy FAQ

 Galaxy Workflow : How to have better output file names ?

Importantly, the following solutions will only work if you take the time to give meaningful names to the workflow input dataset(s) and to the history itself.

  1. Use the rename file action on output files.

This action can take a fixed name but this is quite limited in a number of time. More generally you should build output file names dynamically using one or more of the job's input variable with the #{input_var_name} or with new workflow input variable that will be automatically generated using ${var_name}. One can even manipulate input string with basename, upper and lower e.g. #{ input | basename}

  1. Think about the dynamic file renaming offered by the NFS_transfer tool


What is the FASTQ encoding of the reads GeneCore gave me ?

The sequence data receiving from GeneCore after June 15 2011 is sanger fastq (Phred+33, range 0-41) and before June 15 2011 is illumina fastq (Phred+64, range 0-40). More information about fastq format and quality encoding, please see here