STAR Parameters for TCGA and GTEX

[angarb]

Hey @PhilPalmer,

When we are running TCGA or GTEX data, would it be possible to add a couple parameters to STAR:

1. --outFilterScoreMinOverLread 0.33
2. --outFilterMatchNminOverLread 0.33
3. --alignSJDBoverhangMin 1

Similar to the TCGA parameters - https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/

Does this look ok @lmurba?

[angarb]

@lmurba - did we also want to remove --alignEndsType EndToEnd ? To allow for soft clipping?

[lmurba]

@angarb I think so. I want to test it out first though

[PhilPalmer]

Let me know if you have any questions on this, it should be as easy as #123

[lmurba]

Problem

TCGA, GTEX and potentially other data have poorer quality than our in-house data. As a result, we want to be able to lower the filtering cuttoffs.

Solution

Add two additional parameters to config:
filterScore which controls outFilterScoreMinOverLread and outFilterMatchNminOverLread (int)
sjdOverhangMin which controls alignSJDBoverhangMin (int)

Implementation

• add new parameters filterScore and sjdOverhangMin
  • add new parameters and defaults to nextflow.config (see below)
  • add new parameters to main.nf
    • add new parameters to help message
    • add new parameters to log
    • add to required process and script
  • update usage.md
• test

Defaults for new parameters

filterScore = 0.66
sjdOverhangMin = 3