gigascience/galaxy-tools-bgisoap — pull request #7 by huayan (2013-03-05 07:46:56+00:00)
Title: Huayan

Hi Peter,

I fixed some errors with "full parameter settings". And also the SMD submodules can run as a workflow. For details, please see the following txt file:

Mar. 4, 2013
Pending bugs:
1. soap1:
The parameter -t (read_id) for full parameter settings will lead to an endless loop, so removed this paramter for now.

2. soapsnp
The parameter -q for full parameter settings will lead to an empty output so
an error too. Removed for now.

3. soapdenovo2
The parameter -m (max_k if multi-kmer) is removed due to error.

4. soapdenovo-trans
"reads only used for scaffold assembly" not working
May need to rewrite this tool.

Solved issues:
1. Scaff Submodule
Parameter -z was removed from the command since no such one exists.

2. SoapCoverage:
working now.

3. SOAPSNV package
Able to run the output from one to another, as a workflow.