millironx/taxprofiler
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Moritz E. Beber 2022-10-21 16:36:35 +02:00 committed by GitHub
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docs/usage.md
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@ -92,7 +92,7 @@ Column specifications are as follows:
| Column | Description | | Column | Description |
| ----------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ----------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `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. | | `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. | | `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 profiler that you wish to specify that the taxonomic profiling tool should use when profiling against this specific. Can be empty to use taxonomic 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. | | `db_params` | Any parameters of the given taxonomic profiler that you wish to specify that the taxonomic profiling tool should use when profiling against this specific. Can be empty to use taxonomic 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. |
| `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]. | | `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]. |

4
subworkflows/local/profiling.nf
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@ -41,7 +41,7 @@ workflow PROFILING {
.combine(databases) .combine(databases)
.branch { .branch {
malt: it[2]['tool'] == 'malt' malt: it[2]['tool'] == 'malt'
kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken' kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken' // to reuse the kraken module to produce the input data for bracken
metaphlan3: it[2]['tool'] == 'metaphlan3' metaphlan3: it[2]['tool'] == 'metaphlan3'
centrifuge: it[2]['tool'] == 'centrifuge' centrifuge: it[2]['tool'] == 'centrifuge'
kaiju: it[2]['tool'] == 'kaiju' kaiju: it[2]['tool'] == 'kaiju'
@ -134,6 +134,7 @@ workflow PROFILING {
ch_raw_profiles = ch_raw_profiles.mix( ch_raw_profiles = ch_raw_profiles.mix(
KRAKEN2_KRAKEN2.out.report KRAKEN2_KRAKEN2.out.report
// Set the tool to be strictly 'kraken2' instead of potentially 'bracken' for downstream use. // Set the tool to be strictly 'kraken2' instead of potentially 'bracken' for downstream use.
// Will remain distinct from 'pure' Kraken2 results due to distinct database names in file names.
.map { meta, report -> [meta + [tool: 'kraken2'], report]} .map { meta, report -> [meta + [tool: 'kraken2'], report]}
) )
@ -141,6 +142,7 @@ workflow PROFILING {
if ( params.run_kraken2 && params.run_bracken ) { if ( params.run_kraken2 && params.run_bracken ) {
// remove files from 'pure' kraken2 runs, so only those aligned against bracken2 kraken database are taken for brakcen
def ch_input_for_bracken = KRAKEN2_KRAKEN2.out.report def ch_input_for_bracken = KRAKEN2_KRAKEN2.out.report
.filter { meta, report -> meta['tool'] == 'bracken' } .filter { meta, report -> meta['tool'] == 'bracken' }