Adds xstag strType parameter

[Vlad-Dembrovskyi]

Closes #201

(PR closed without merging in favor of cleaner PR: #264 )

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]

It was found that stringti_merged results folder as well as some other folders are missing all or some files. Most probably that started happening after output pattern update needed to save .command.* logs in #251 . Debugging the issue.

[Vlad-Dembrovskyi]

https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/1c47991176b3dbb1e934a55cfb3e4cf998614448/main.nf#L993-L996

Before:

After:

[Vlad-Dembrovskyi]

https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/1c47991176b3dbb1e934a55cfb3e4cf998614448/main.nf#L745-L748

Before:

After:

[Vlad-Dembrovskyi]

https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/1c47991176b3dbb1e934a55cfb3e4cf998614448/main.nf#L777-L779

Before: https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/1c47991176b3dbb1e934a55cfb3e4cf998614448/main.nf#L770

After: https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/b66535f57c1179fcd188901b2e7ea9349bfa2ea7/main.nf#L770

[Vlad-Dembrovskyi]

PR closed without merging in favor of cleaner PRs:

263

264