Viraj Deshpande issues

Results 5 issues of


                                            Viraj Deshpande

Add cwd argument to addWorkflowTask

Currently, I can use "cwd" argument as shown in the cwd demo for "addTask", but it gives me an error "unexpected keyword argument" if I use it with "addWorkflowTask".

Extracting reads/read pairs mapping to fusions

What is the best way to obtain the reads/read pairs mapping across fusion junctions? Does the pseudobam file from kallisto indicate alignment of mate to another transcript in the same...

Duplicate cycles reported

In some cases, AA reports duplicate cycles in cycles.txt file. For example, see FF-55_amplicon1_cycles.txt in the run14 set

Docker support for paths with spaces

Current implementation does not propagate spaces or special characters in arguments to docker script.

Sharding Cram files and inputting multiple datasets simultaneously

Hello Vadim, Sorry for the delay, I was distracted by some other stuff. The patch I have added is a very small one. The only external change to CramTools is...