Feature #4743

[Crunch] Upgrade run-command regex or basename for stricter file argument ordering

Added by Bryan Cosca over 6 years ago. Updated over 1 year ago.

Assigned To:
Target version:
Start date:
Due date:
% Done:


Estimated time:
Story points:


Currently, the convention I use to group paired end reads together would be to group by (.*)[12]. so foo_1 and foo_2 can be paired as well as foo.1 and foo.2 in their group. I run into a problem where I cannot specify which read I would like in what place when running a program because of a couple reasons: the groups are not alphabetical, sometimes the group indexes foo_2 and then foo_1 (for example: qr1hi-8i9sb-kdry51qdiy9tb42). If I want to run a program s.t. prog.py foo_1 foo_2 is necessary, I'm unable to do so. I also cannot grab the basename of foo_1 and foo_2 because the basename function does not separate by "_". The current workaround would be to glob the basename of files but that only works with periods. i.e. prog.py foo.1 foo.2 is possible because i can grab foo and search for foo.1 and search for foo.2.

Related issues

Related to Arvados - Bug #4562: [Documentation] Wiki page: explain appropriate use cases for arv-run vs. run-command vs. writing your own crunch script.Resolved01/16/2015


#1 Updated by Tom Clegg over 6 years ago

Current options include:
  • Separate component that rearranges/renames input files to make them easier for run-command to work with
  • Transition from run-command to a Python program (would be better if we could make this easier/smoother)

#2 Updated by Brett Smith over 6 years ago

  • Subject changed from Run-command upgraded regex or basename to [Crunch] Upgrade run-command regex or basename for stricter file argument ordering
  • Category set to Crunch

#3 Updated by Peter Amstutz over 1 year ago

  • Status changed from New to Closed

Also available in: Atom PDF