Change the input files to only take one transcriptome assembly file instead of two #47
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keithchev
approved these changes
Jun 5, 2024
demo/README.md
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| We pulled the "short contigs" file from an internal S3 bucket. | ||
| It contains contigs that were filtered from the Amblyomma transcriptome prior to txome merging. | ||
| We also pulled short contigs (less than 75 bp) from an internal S3 bucket and added these contigs to the `contigs.fa` file (50 contigs). | ||
| These are contigs that were filtered from the *Amblyomma* transcriptome prior to transcriptome merging (mid assembly pipeline). |
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Consider clarifying what "mid assembly pipeline" means (afaict, it's also not clear from this readme what pipeline this is referring to)
demo/config.yml
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| # ORFs should be predicted from the same transcriptome assembly as the "contigs" input file. | ||
| # ORFs should have the same name (before the first period in the name) as the contigs in the | ||
| # "contigs" input file. TransDecoder provides files in the proper format. | ||
| # Used for cleavage peptide prediction and annotation of nonribosomal peptide synthetases, and to | ||
| # remove coding transcripts from the transcriptome assembly before sORF prediction. | ||
| # - orfs_nucleotides: predicted ORFs as nucleotide sequences. Should contain the same ORFs as | ||
| # "orfs_amino_acids" but in nucleotide format. TransDecoder also provides this file in the proper | ||
| # format. If this file contains short ORFs (< 300 nucleotides), they will not be reported as sORFs | ||
| # as they are already annotated in the input. | ||
| # - plmutils_model_dir: path to the directory for the plmutils model that will predict whether sORFs | ||
| # are coding or non-coding. |
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This is unrelated to this PR, but fwiw I feel you could delete all of these comments in this demo config (so that they only appear in one place, in the main top-level config.yml). This would avoid duplicating them (and avoid the need to keep them in sync when they are changed)
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oh i love this, I'll do that, thank you!
Co-authored-by: Keith Cheveralls <[email protected]> Signed-off-by: Taylor Reiter <[email protected]>
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PR checklist
Fixes #123, Resolves #456).condaenvironments.PR description