stringtie subworkflow and gffcompare #85
Conversation
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Looks good to me but can't be tested yet, Do we keep this open until it can be tested? I guess it won't pass anyway |
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Tests pass but the subworkflow is not being called... I'll check why |
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How do feel @karlaarz @Emeerdink about adding featurecounts after the stringtie merge step? That way we can quantify the types of transcripts we capture |
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yes, it is a good idea. I can add both htseq and featurecounts modules. |
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Would you do this before the GFFcompare steps There are many filtering and merging steps that happen in the old pipeline before counting. What are your thoughts on that? |
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yes, it can be added before or after gffcompare as in any case the input should be stringtie's output. I would suggest to add it after gffcompare now that all the checks of these modules have passed. What do you think? |
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Beware! Checks are passing but the stringtie+gffcompare modules are not being run, and I'm still trying to troubleshoot why |
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Ah sorry, my bad, I would add the counting after the gffcompare and all the filtering of the annotation files. This is what happens in the current pipeline (counting all the way at the end). in this paper, they do the counting directly after the merging of annotations and the filtering of the lncRNA annotations is done in a separate track. We can consider this as an update of the pipeline. |
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Oooookey, the tests are passing and the stringtie and gffcompare modules are being correctly executed 🥳 The changes needed for the modules to run were purely structural: some channel factories needed to be changed. I would now merge this PR, since the scope and changes are big and substantial. I would also add htseqcount and featurecounts, but would do it on another separate PR. |
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@ctuni @Emeerdink I can work on the htseq and featurecounts modules later on today/tomorrow considering this paper |
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).