Opened 9 years ago

Closed 9 years ago

#654 closed enhancement (fixed)

Synchronize default options for pipeline analysis

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: minor Milestone: Reggie v2.16.1
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The reggie-ogs-hosts.xml file contain a lot of options for the programs used in the analysis pipeline. The current version is based on an older setup and some parameters have been changed.

Change History (9)

comment:1 by Nicklas Nordborg, 9 years ago

(In [2763]) References #654: Synchronize default options for pipeline analysis

Updated parameters for trimmomatic in the demux step.

comment:2 by Nicklas Nordborg, 9 years ago

(In [2764]) References #654: Synchronize default options for pipeline analysis

Updated path to ribo_phix_repeats_filter.

comment:3 by Nicklas Nordborg, 9 years ago

(In [2765]) References #654: Synchronize default options for pipeline analysis

Updated path to reference folder.

comment:4 by Nicklas Nordborg, 9 years ago

(In [2766]) References #654: Synchronize default options for pipeline analysis

Updated path to Picard folder.

comment:5 by Nicklas Nordborg, 9 years ago

(In [2767]) References #654: Synchronize default options for pipeline analysis

Updated path to pipeline scripts folder.

comment:6 by Nicklas Nordborg, 9 years ago

(In [2768]) References #654: Synchronize default options for pipeline analysis

Updated paths data folders.

comment:7 by Nicklas Nordborg, 9 years ago

(In [2771]) References #654: Synchronize default options for pipeline analysis

Updated tophat options.

comment:8 by Nicklas Nordborg, 9 years ago

(In [2772]) References #654: Synchronize default options for pipeline analysis

Same changes applied to trunk version of configuration file. Since the file has moved changes would not have been merged back to the trunk automatically.

comment:9 by Nicklas Nordborg, 9 years ago

Resolution: fixed
Status: newclosed
Note: See TracTickets for help on using tickets.