Question: File Formats In Workflows
gravatar for PaulW
8.5 years ago by
PaulW60 wrote:
Hi, Was impressed by the Worflow screencasts but when I converted my history to a workflow it failed. This is because some of the tools output tabular data, but some downstream tools require interval format input and therefore fail. When I made the history I manually changed the file format and nominated the fields for chr,start,end,strand, but this is lost in the workflow. Obvious ideas: * Use a tabular-to-interval tool - I looked but can't find one * Only used tools which output interval format - a less desirable solution. e.g. I can't figure out how to filter out duplicate codons in my gene-BED-to-codon-BED file except using the statistics->count function which outputs tabular. Has anyone worked out how to change formats within a workflow? regards, Paul
ADD COMMENTlink modified 8.5 years ago by Dannon Baker3.7k • written 8.5 years ago by PaulW60
gravatar for Dannon Baker
8.5 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:
Paul, We're working on a new feature that'll allow extra actions within workflows that should cover this case, and it will be available soon. Regarding a workaround for this specific scenario, would you mind sharing the workflow with '' ? That way I can take a look and see if I can come up with something that'll work for you in the short term, as well as verifying that the new workflow actions will handle the task. Thanks for using Galaxy, -Dannon
ADD COMMENTlink written 8.5 years ago by Dannon Baker3.7k
Dannon, Thanks for your interest. It would be a handy feature to be able to attach metadata to tabular files in the workflow. I have shared the workflow. It is called 'chr21 analysis'. Input is a gene BED file for a chromosome region from UCSC data (which includes gene variants). Workflow fails after I use "count" to get only unique records from my codon file. The other input is a list of SNPs in the same region. regards, Paul
ADD REPLYlink written 8.5 years ago by PaulW60
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