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TheJacksonLaboratory / splicing-pipelines-nf

Repository for the Anczukow-Lab splicing pipeline
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Adds xstag strType parameter (clean pr) #264

Closed Vlad-Dembrovskyi closed 2 years ago

Vlad-Dembrovskyi commented 2 years ago

Closes #201

(This PR is cleaner version of #261)

This PR

Makes strType parameter in xs command (after star, in star process) to be not hardcoded as 2 but be set depending on value of stranded parameter.

To test:

git clone https://github.com/TheJacksonLaboratory/splicing-pipelines-nf
cd splicing-pipelines-nf
git checkout add-xs-tag
# Default execution, same as if strType=2 was hardcoded
NXF_VER=20.01.0 nextflow run . -profile ultra_quick_test,docker -resume --stranded 'first-strand'
NXF_VER=20.01.0 nextflow run . -profile ultra_quick_test,docker -resume --stranded 'second-strand'
Vlad-Dembrovskyi commented 2 years ago

Correct XS tag functionality was approved by @angarb on a call on 7th Sep. Merging.