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Merge pull request #237 from nf-core/bracken-params
Support Kraken and Bracken db_params in database sheet
This commit is contained in:
James A. Fellows Yates
GitHub
commit
45ac6fedc2
4 changed files with 61 additions and 13 deletions
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@ -355,6 +355,7 @@ process {
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withName: BRACKEN_BRACKEN {
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errorStrategy = 'ignore'
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
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publishDir = [
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path: { "${params.outdir}/bracken/${meta.db_name}/" },
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@ -95,7 +95,7 @@ An example database sheet can look as follows, where 5 tools are being used, and
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tool,db_name,db_params,db_path
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malt,malt85,-id 85,/<path>/<to>/malt/testdb-malt/
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malt,malt95,-id 90,/<path>/<to>/malt/testdb-malt.tar.gz
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bracken,db1,,/<path>/<to>/bracken/testdb-bracken.tar.gz
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bracken,db1,;-r 150,/<path>/<to>/bracken/testdb-bracken.tar.gz
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kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
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krakenuniq,db3,,/<path>/<to>/krakenuniq/testdb-krakenuniq.tar.gz
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centrifuge,db1,,/<path>/<to>/centrifuge/minigut_cf.tar.gz
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@ -103,14 +103,16 @@ metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/
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motus,db_mOTU,,/<path>/<to>/motus/motus_database/
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```
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For Bracken, if you wish to supply any 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.
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Column specifications are as follows:
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| Column | Description |
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| ----------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| `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. |
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| `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. |
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| `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. |
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| `db_path` | Path to the database. Can either be a path to a directory containing the database index files or a `.tar.gz` file which contains the compressed database directory with the same name as the tar archive, minus `.tar.gz` [required]. |
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| Column | Description |
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| ----------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| `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. |
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| `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. |
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| `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. |
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| `db_path` | Path to the database. Can either be a path to a directory containing the database index files or a `.tar.gz` file which contains the compressed database directory with the same name as the tar archive, minus `.tar.gz` [required]. |
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> 💡 You can also specify the same database directory/file twice (ensuring unique `db_name`s) and specify different parameters for each database to compare the effect of different parameters during classification/profiling.
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@ -13,8 +13,8 @@ workflow DB_CHECK {
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ch_dbs_for_untar = Channel.empty()
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ch_final_dbs = Channel.empty()
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// special check to check _between_ rows, for which we must group rows together
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// note: this will run in parallel to within-row validity, but we can assume this will run faster thus will fail first
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// Special check to check _between_ rows, for which we must group rows together
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// Note: this will run in parallel to within-row validity, but we can assume this will run faster thus will fail first
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Channel.fromPath(dbsheet)
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.splitCsv ( header:true, sep:',' )
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.map {[it.tool, it.db_name] }
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@ -25,7 +25,7 @@ workflow DB_CHECK {
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if ( unique_names.size() < db_name.size() ) exit 1, "[nf-core/taxprofiler] ERROR: Each database for a tool must have a unique name, duplicated detected. Tool: ${tool}, Database name: ${unique_names}"
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}
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// normal checks for within-row validity, so can be moved to separate functions
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// Normal checks for within-row validity, so can be moved to separate functions
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parsed_samplesheet = Channel.fromPath(dbsheet)
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.splitCsv ( header:true, sep:',' )
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.map {
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@ -40,7 +40,7 @@ workflow DB_CHECK {
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}
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// Filter the channel to untar only those databases for tools that are selected to be run by the user.
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ch_input_untar = ch_dbs_for_untar.untar.dump()
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ch_input_untar = ch_dbs_for_untar.untar
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.filter {
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params["run_${it[0]['tool']}"]
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}
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@ -71,6 +71,9 @@ def validate_db_rows(LinkedHashMap row){
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if ( row.db_params.contains('"') ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
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if ( row.db_params.contains("'") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
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// check if any form of bracken params, that it must have `;`
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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}"
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}
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def create_db_channels(LinkedHashMap row) {
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@ -120,8 +120,27 @@ workflow PROFILING {
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}
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if ( params.run_kraken2 ) {
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// Have to pick first element of db_params if using bracken,
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// as db sheet for bracken must have ; sep list to
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// distinguish between kraken and bracken parameters
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ch_input_for_kraken2 = ch_input_for_profiling.kraken2
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.dump(tag: "ch_input_for_kraken2_b4")
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.map {
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meta, reads, db_meta, db ->
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def db_meta_new = db_meta.clone()
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ch_input_for_kraken2 = ch_input_for_profiling.kraken2
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// Only take second element if one exists
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def parsed_params = db_meta_new['db_params'].split(";")
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if ( parsed_params.size() == 2 ) {
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db_meta_new['db_params'] = parsed_params[0]
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} else if ( parsed_params.size() == 0 ) {
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db_meta_new['db_params'] = ""
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} else {
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db_meta_new['db_params'] = parsed_params[0]
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}
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[ meta, reads, db_meta_new, db ]
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}
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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@ -160,10 +179,33 @@ workflow PROFILING {
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.filter { meta, db -> meta['tool'] == 'bracken' }
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.map { meta, db -> [meta['db_name'], meta, db] }
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// Extract the database name to combine by.
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// Combine back with the reads
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ch_input_for_bracken = ch_kraken2_output
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.map { meta, report -> [meta['db_name'], meta, report] }
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.combine(ch_bracken_databases, by: 0)
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.map {
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key, meta, reads, db_meta, db ->
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def db_meta_new = db_meta.clone()
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// Have to pick second element if using bracken, as first element
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// contains kraken parameters
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if ( db_meta['tool'] == 'bracken' ) {
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// Only take second element if one exists
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def parsed_params = db_meta_new['db_params'].split(";")
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if ( parsed_params.size() == 2 ) {
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db_meta_new['db_params'] = parsed_params[1]
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} else {
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db_meta_new['db_params'] = ""
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}
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} else {
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db_meta_new['db_params']
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}
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[ key, meta, reads, db_meta_new, db ]
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}
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.multiMap { key, meta, report, db_meta, db ->
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report: [meta + db_meta, report]
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db: db
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