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Fix kraken db loading fromPath #673

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Merged
apeltzer merged 7 commits into from
Feb 3, 2021
Merged

Fix kraken db loading fromPath #673

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0468dfa
fix kraken db loading fromPath
Feb 1, 2021
ee88d1c
Merge branch 'dev' of github.com:nf-core/eager into dev
Feb 1, 2021
1fd116d
update changelog
Feb 1, 2021
f8fa322
change basenaming of database
Feb 1, 2021
6724770
renaming archive files in decomp kraken
Feb 1, 2021
fea3249
handle case when files are already in $dbdir
Feb 2, 2021
d89b4cc
transforms to value channel with .first()
Feb 3, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- [#631](https://github.com/nf-core/eager/issues/631): - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled
- Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv
- Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data. `
- [#673](https://github.com/nf-core/eager/pull/673): Fix Kraken database loading when loading from directory instead of compressed file.

### `Dependencies`

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6 changes: 4 additions & 2 deletions main.nf
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Expand Up @@ -3108,14 +3108,16 @@ if (params.run_metagenomic_screening && params.database.endsWith(".tar.gz") && p
path(dbname) into ch_krakendb

script:
dbname = params.database.tokenize("/")[-1].tokenize(".")[0]
dbname = ckdb.toString() - '.tar.gz'
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"""
tar xvzf $ckdb
mkdir -p $dbname
mv *.k2d $dbname || echo "nothing to do"
"""
}

} else if (! params.database.endsWith(".tar.gz") && params.run_metagenomic_screening && params.metagenomic_tool == 'kraken') {
ch_krakendb = path(params.database)
ch_krakendb = Channel.fromPath(params.database).first()
} else {
ch_krakendb = Channel.empty()
}
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