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Adjusted handling of compressed tar archive containing kraken2 database #54

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Jun 23, 2020
Merged

Adjusted handling of compressed tar archive containing kraken2 database #54

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c3d8a46
Adjusted handling of kraken2 dbs to changes names
skrakau Jun 22, 2020
7ec13a4
Updated CHANGELOG
skrakau Jun 22, 2020
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- Fix missing MultiQC when `--skip_quast` or `--skip_busco` was specified
- Fix missing channels when `--keep_phix` is specified
- Added missing parameters to summary
- Updated links to minikraken db
- Fixed kraken2 dp preparation: allow different names for compressed archive file and contained folder as for some minikraken dbs

### `Deprecated`

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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -228,7 +228,7 @@ Database for taxonomic binning with centrifuge (default: none). E.g. "<ftp://ftp

### `--kraken2_db`

Database for taxonomic binning with kraken2 (default: none). E.g. "<ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_v2_8GB_201904_UPDATE.tgz>"
Database for taxonomic binning with kraken2 (default: none). E.g. "<ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz>"

### `--cat_db`

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4 changes: 2 additions & 2 deletions main.nf
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Expand Up @@ -70,7 +70,7 @@ def helpMessage() {

Taxonomy:
--centrifuge_db [file] Database for taxonomic binning with centrifuge (default: none). E.g. "ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz"
--kraken2_db [file] Database for taxonomic binning with kraken2 (default: none). E.g. "ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_v2_8GB_201904_UPDATE.tgz"
--kraken2_db [file] Database for taxonomic binning with kraken2 (default: none). E.g. "ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz"
--skip_krona [bool] Skip creating a krona plot for taxonomic binning
--cat_db [file] Database for taxonomic classification of metagenome assembled genomes (default: none). E.g. "tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190108.tar.gz"
The zipped file needs to contain a folder named "*taxonomy*" and "*CAT_database*" that hold the respective files.
Expand Down Expand Up @@ -777,7 +777,7 @@ process kraken2_db_preparation {
file(db) from file_kraken2_db

output:
set val("${db.baseName}"), file("${db.baseName}/*.k2d") into kraken2_database
set val("${db.baseName}"), file("*/*.k2d") into kraken2_database

script:
"""
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