Closed JohnHadish closed 2 years ago
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nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 05a78c0
+| ✅ 73 tests passed |+
#| ❔ 27 tests were ignored |#
!| ❗ 1 tests had warnings |!
With the fixes to the documentation, paired end issue, nf-core liniting and a few other tweaks this looks good to go!
This makes it so the dsl2 version of GEMmaker (currently dev) can run STAR. This does not correct issue #252, so like all pipelines besides Kallisto, STAR will only run on single end reads.
Testing: Test using the 3 Arabidopsis runs from the [GEMmaker documentation]()
1) Put these files in a file called "SRAs.txt"
2) Download Arabidopsis genome and gtf files
3) Create an Arabidopsis Genome Index for STAR. This will take ~3 min
4) Now Run Using the SRAs.txt and your new index files for Arabidopsis from the Star branch of GEMmaker. This will take ~12 min
Look at results
Notes: