Update documentation to include db_type #535
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jfy133
reviewed
Sep 26, 2024
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
jfy133
reviewed
Sep 26, 2024
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Oh and in the table itself |
jfy133
reviewed
Sep 26, 2024
| motus,db_mOTU,,/<path>/<to>/motus/motus_database/ | ||
| ganon,db1,,/<path>/<to>/ganon/test-db-ganon.tar.gz | ||
| kmcp,db1,;-I 20,/<path>/<to>/kmcp/test-db-kmcp.tar.gz | ||
| tool,db_name,db_params,db_type,db_path |
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Myabe give a second example without the db_type column
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Added this for malt.
docs/usage.md
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| @@ -157,6 +157,7 @@ Column specifications are as follows: | |||
| | `tool` | Taxonomic profiling tool (supported by nf-core/taxprofiler) that the database has been indexed for [required]. Please note that `bracken` also implies running `kraken2` on the same database. | | |||
| | `db_name` | A unique name per tool for the particular database [required]. Please note that names need to be unique across both `kraken2` and `bracken` as well, even if re-using the same database. | | |||
| | `db_params` | Any parameters of the given taxonomic classifier/profiler that you wish to specify that the taxonomic classifier/profiling tool should use when profiling against this specific database. Can be empty to use taxonomic classifier/profiler defaults. Must not be surrounded by quotes [required]. We generally do not recommend specifying parameters here that turn on/off saving of output files or specifying particular file extensions - this should be already addressed via pipeline parameters. For Bracken databases, must at a minimum contain a `;` separating Kraken2 from Bracken parameters. | | |||
| | `db_type` | A column to distinguish between short- and long-read databases. If the column is empty, the pipeline will assume all databases (and their settings specified in `db_params`!) will be applicable for both short and long read data [optional]. | | |||
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@LilyAnderssonLee what are the valid values ehre? short long and short;long?
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You are right. And the default is short;long
Co-authored-by: James A. Fellows Yates <[email protected]>
…xprofiler into documentation_release
jfy133
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Sep 26, 2024
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Almost there! @LilyAnderssonLee can you also review for accuracy?
| metaphlan,db1,,short,/<path>/<to>/metaphlan/metaphlan_database/ | ||
| motus,db_mOTU,,long,/<path>/<to>/motus/motus_database/ | ||
| ganon,db1,,short,/<path>/<to>/ganon/test-db-ganon.tar.gz | ||
| kmcp,db1,;-I 20,short,/<path>/<to>/kmcp/test-db-kmcp.tar.gz | ||
| ``` |
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Add a second csv example block but without the db_type column (essentially the one from before you edited).
Sorry this is what I meant before about having an example without this
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I updated the PR with two example blocks.
docs/usage.md
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| kmcp,db1,;-I 20,/<path>/<to>/kmcp/test-db-kmcp.tar.gz | ||
| tool,db_name,db_params,db_type,db_path | ||
| malt,malt85,-id 85,short,/<path>/<to>/malt/testdb-malt/ | ||
| malt,malt95,-id 90,,/<path>/<to>/malt/testdb-malt.tar.gz |
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I think if the column is in, it has to be filled (@LilyAnderssonLee do you remember). If you want both you need short;long as befote.
See my comment below about what I had actually meant
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Yes, if the db_type column is included in the database.csv, it should be filled with one of the following values: short, long, or short;long. If the db_type column is missing from the database.csv, it will take the default short;long.
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I have updated the PR based on your comments.
Co-authored-by: James A. Fellows Yates <[email protected]>
jfy133
approved these changes
Oct 1, 2024
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This PR updates the documentation to describe the
db_typecolumn that has been added in database samplesheet.PR checklist
nf-core 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).