search

BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
20 stars 11 forks source link

salmon does not produce sa.bin files -> pos.bin #79

Closed smoe closed 3 years ago

smoe commented 3 years ago

Hello,

I could not find the exact version of salmon you are expecting. The test samples give a reference to 0.9.0 - but that seems like from quite a while ago. Running salmon 1.3.0 I had a problem with the expected sa.bin files which just do not manifest themselves even though salmon completed successfully. I also failed to locate them in the salmon source tree - gone? I took some creative freedom to change this to pos.bin.

If I am not mistaken and you prefer remain compatible with your current setup, would there then be a reasonable way to have your pipeline run in a salmon-version-agnostic way? Alternatively, you could check the version and adjust the copying/testing behaviour?

$ salmon --version
salmon 1.3.0

The attached patch helps over here to survive the build testing.

Kind regards, Steffen

rekado commented 3 years ago

This looks good to me. Thank you!

borauyar commented 3 years ago

Sorry, I forgot about this pull request, but fixed the salmon index issue here (https://github.com/BIMSBbioinfo/pigx_rnaseq/commit/c8e93f294ee21ee380d8fe9339129e7e9b6babf9)