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ewels / clusterflow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
https://ewels.github.io/clusterflow/
GNU General Public License v3.0
97 stars 27 forks source link

Create salmon.cfmod.pl #114

Closed darogan closed 7 years ago

darogan commented 7 years ago

New module for salmon quasi-mapping

ewels commented 7 years ago

Fast work! :) Few more things I've just thought of:

  1. Doesn't look like there are any pipelines that use the module, could you quickly create one or two?
  2. Could you add it to the list of supported tools in README.md? Looks like I've broken the markdown actually, so happy to do this myself if you have any trouble.
  3. Please add yourself to the list of contributors at the bottom of the readme 😁

Phil

darogan commented 7 years ago

I'm running some RNA-Seq benchmarks as part of projects I'm working on so I'll be creating modules for gsnap, subreads and erne. I'll submit when I've got them running and tested.

I'll make a fastq_salmon pipeline now

ewels commented 7 years ago

Thanks! Was about to merge, but noticed that the Travis test is failing..

The test script says that it can't get the module requirements properly:

/home/travis/build/ewels/clusterflow/source/CF/../../modules/salmon.cfmod.pl cores not set
/home/travis/build/ewels/clusterflow/source/CF/../../modules/salmon.cfmod.pl memory not set
/home/travis/build/ewels/clusterflow/source/CF/../../modules/salmon.cfmod.pl time not set
Command for testing:
/home/travis/build/ewels/clusterflow/source/CF/../../modules/salmon.cfmod.pl --requirements --run_fn /home/travis/build/ewels/clusterflow/source/CF/../../clusterflow.config --cores 8 --mem 128G

Any idea what's going on?

darogan commented 7 years ago

I'm not sure of the error. I just uploaded a new version of the file. Ignore the one previous to this.