Question: How do I automagically make informative dataset names at different workflow stages?
2
gravatar for cgibas
4.4 years ago by
cgibas20
United States
cgibas20 wrote:

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.

workflow renaming datasets • 1.4k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by cgibas20

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

ADD REPLYlink written 2.7 years ago by marc.ciosi0
1
gravatar for Dannon Baker
4.4 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

There's a (rather barebones, for the moment) wiki page explaining some of the syntax for the rename options, but the short answer is that you need the actual tool's input ids.  For FastQC, those ids are 'input_file' and 'contaminants', and for FastQ Groomer it is also 'input_file'.

So, you'd want something like #{input_file).groomed

I've just committed a few updates to this functionality to list the available inputs in the workflow editor, so this should be easier in the future.

ADD COMMENTlink written 4.4 years ago by Dannon Baker3.7k

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

ADD REPLYlink written 2.7 years ago by marc.ciosi0

What is the tool input id for merge collections, I am having the same issue using workflow variables with it.

Thank you.

Regards, Sara

ADD REPLYlink written 3 months ago by SOneil40
0
gravatar for cgibas
4.4 years ago by
cgibas20
United States
cgibas20 wrote:

Thanks, it worked.  It'll definitely be helpful to have easy access to those variables in the workflow editor.

ADD COMMENTlink written 4.4 years ago by cgibas20
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