Implement process to detect strandedness of input RNAseq data

[imendes93]

Description

This Pull Request aims to implement a chain of processes to determine the strandedness of the RNA-seq library being used. This PR closes #314

Added Features

• Add container with the necessary dependencies for strandedness prediction (salmon)
• Add process to infer strandedness
  • Uncompress salmon index
  • Quantify reads using salmon and save bam file
  • Grep strandedness information from Salmon output (grep log file)
  • Translate strandedness prediction into first-strand, second-strand and false
• Integrate strandedness prediction into workflow logic

[imendes93]

Post on strandedness detection with STAR, Kallisto and Salmon: https://littlebitofdata.com/en/2017/08/strandness_in_rnaseq/

[cgpu]

@imendes93 thank you for the addition. Have we added a ci test that tests the newly added functionality?

[imendes93]

@imendes93 thank you for the addition. Have we added a ci test that tests the newly added functionality?

Not yet @cgpu as still some items are pending from the Issue list above. Will add a new profile to test strandedness asap!

[cimendes]

@cgpu profile with strandedness test was not added to the ci matrix