merge the lncpipe:dev to original LncPipe:dev #36 - #37
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Adding the necessary github files
the pipeline now reads a samplesheet!
added structure based on old pipeline
added backbone
backbone added 1
stringtie subworkflow and gffcompare. Went through extensive testing by @ctuni
Added subread_featurecounts and htseq modules
Automated security rollout could not apply this cleanly. Resolve the remaining conflict markers and *.rej files, then open a PR from 'patch' into 'dev'. Patch source: this pipeline's TEMPLATE branch never received the nf-core/tools 4.0.3 sync, so the change was taken from nf-core/abotyper's TEMPLATE with the repository identity in branch.yml rewritten for this pipeline. While resolving, check that no file ended up naming nf-core/abotyper. Note: these files had their conflicts resolved for you, by resetting them wholesale to the nf-core/tools 4.0.3 template version — so they carry no markers even though they conflicted. Review them: .github/workflows/branch.yml .github/workflows/template-version-comment.yml
Remove vulnerable PR-comment artifact pattern
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