testdata for bacmodel pipeline #2060
Conversation
| @@ -0,0 +1,35 @@ | |||
| # nf-core/bacmodel Test Dataset | |||
There was a problem hiding this comment.
Recommendation: rather than a nested bacmodel/README.md, replace the root README.md of the branch with this content (matching sarek, rnaseq, atacseq, ampliseq, which all use a single root README scoped to the pipeline). Once the files move out of the bacmodel/ subdirectory, this README naturally becomes the branch's top-level one.
There was a problem hiding this comment.
Hi @pinin4fjords ! Thanks a lot for such detailed comments and suggestions! I tried to apply all this
| ## Test Genome | ||
|
|
||
| **Species:** _Faecalibacterium taiwanense_ | ||
| **Source:** BIP-2026-46 Silva Assemblies (IKMB, sample 3606MB_1118_055_H10) |
There was a problem hiding this comment.
BIP-2026-46 / IKMB sample 3606MB_1118_055_H10 looks like an internal sample identifier. For a public test-datasets branch it would be helpful to cite either a public NCBI/ENA accession for the assembly (so reviewers can re-derive it) or a one-line note confirming permission to redistribute publicly. Compare with the rnaseq/atacseq READMEs which link to GEO/SRA/PubMed.
| **Source:** BIP-2026-46 Silva Assemblies (IKMB, sample 3606MB_1118_055_H10) | ||
| **Assembly:** Bacterial isolate genome assembly | ||
| **Size:** ~2.7 Mbp (13 contigs) | ||
| **File:** `faecalibacterium_taiwanense.fasta.gz` |
There was a problem hiding this comment.
Worth adding a short "Sampling procedure" section here, in the style of the rnaseq and atacseq READMEs. Even if the assembly is used unmodified, an explicit note saying so ("used as-is, ~2.7 Mbp / 13 contigs, no subsetting applied") helps future maintainers who need to refresh or regenerate the test data.
|
|
||
| ```tsv | ||
| sample fasta | ||
| faecalibacterium_taiwanense https://raw.githubusercontent.com/nf-core/test-datasets/bacmodel/bacmodel/testdata/faecalibacterium_taiwanense.fasta.gz |
There was a problem hiding this comment.
The double bacmodel/bacmodel/ in this URL is the giveaway that the pipeline-name subdirectory is redundant. Once files move to the branch root, this would become https://raw.githubusercontent.com/nf-core/test-datasets/bacmodel/testdata/faecalibacterium_taiwanense.fasta.gz.
| @@ -0,0 +1,2 @@ | |||
| sample fasta | |||
| faecalibacterium_taiwanense https://raw.githubusercontent.com/nf-core/test-datasets/bacmodel/bacmodel/testdata/faecalibacterium_taiwanense.fasta.gz | |||
There was a problem hiding this comment.
Same double bacmodel/bacmodel/ as in the README - flattens out once the layout moves to the branch root.
2 participants
This directory contains test data for the nf-core/bacmodel pipeline, which performs functional annotation and metabolic modeling of bacterial genomes.
The test dataset consists of a complete bacterial genome assembly from Faecalibacterium taiwanense. This species contains diverse functional features including secondary metabolite biosynthesis, carbohydrate-active enzymes, and well-characterized metabolic pathways - enabling comprehensive testing of all bacmodel annotation and modeling tools.