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Relax strictness so can supply empty db_params but block if only single parameter with out ;

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This commit is contained in:
James Fellows Yates 2023-02-08 15:44:37 +01:00
parent fe3d42ffd7
commit b3837cce5b
2 changed files with 3 additions and 2 deletions
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2
docs/usage.md
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@ -103,7 +103,7 @@ metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/
motus,db_mOTU,,/<path>/<to>/motus/motus_database/
```
Bracken **must** have a _semi-colon_ `;` list as in `db_params`, regardless of whether you have parameters or not. This is to allow to specify the Kraken2 parameters before, and Bracken parameters after the `;` as Bracken is a two step process. This is particularly important if you supply a Bracken database with a non-default read length parameter.
For Bracken, if you wish to supply amy parameters to either the Kraken or Bracken step you **must** have a _semi-colon_ `;` list as in `db_params`. This is to allow to specify the Kraken2 parameters before, and Bracken parameters after the `;` as Bracken is a two step process. This is particularly important if you supply a Bracken database with a non-default read length parameter. If you do not have any parameters to specify, you can leave this as empty.
Column specifications are as follows:

3
subworkflows/local/db_check.nf
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@ -71,7 +71,8 @@ def validate_db_rows(LinkedHashMap row){
if ( row.db_params.contains('"') ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
if ( row.db_params.contains("'") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
if ( row.tool == 'bracken' && !row.db_params.contains(";") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. Bracken requires a semi-colon. Error in: ${row}"
// check if any form of bracken params, that it must have `;`
if ( row.tool == 'bracken' && row.db_params && !row.db_params.contains(";") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. Bracken requires a semi-colon if passing parameter. Error in: ${row}"
}