Bug fix update nonredundant output #69
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…d extra folder redundancy while publishing
… redundancy removal mechanisms are both off
…tructured full raw and filtered MSA folders
…ues tuned, output.md updated
…threshold default fixed, rocrate
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Looks good, with two small grammar things.
I'm not requesting a change, but something to consider: I prefer more informative suffixes than .fas (.faa to show it's amino acid fasta) and .aln (typically used for phylip but you have fasta I believe; I use .alnfaa for this).
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
This is a genuinely valid point. I like it! I went through the existing nf-core modules and there are 59 that use .faa but only 4 that utilise .alnfaa. For now, I'll change some of my local modules to output .faa, but I don't think the used tools allow for .alnfaa, yet. Keeping that in mind and while moving forward though, I'll try to start implementing these, wherever possible, in future nf-core modules. Thanks :D |
Fixes #68
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).