I have a collection of 16 FASTQ files that I have made into a list as input to a simple workflow. For the purpose of testing this out, each of the files is going to have two things happen to it -- first, run FastQ Groomer, second, run FastQC. I would like to get some tips on renaming the output so it's easier to keep track of. Originally as uploaded, each of the files is named something like:
31: CMCP6_2HS_reverse_unpaired.red.fastq
Instead of my 16 outputs at each step being named something like "67: FastQ Groomer on 33" or what have you, I would like my datasets to be named in a way that is easy to interpret, like:
67: CMCP6_2HS_reverse_unpaired.red.fastq.groomed
I have only been able to find partial documentation of this in forum and mailing list threads, my understanding is that I should be using something like #{input}.groomed in the rename tool. However, that must not be the real name of my tool input, because using it results in an empty field in the dataset name and a request to enter a value for that variable at the start of the workflow.
Can someone help with this or give me a pointer to better documentation? Thanks.
Could you specify which file name renaming tool you are talking about? I have tried to look for one in the main tools as well as in the tool shed but did not find any. thanks in advance