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Update centrifuge/centrifuge #1495

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merged 11 commits into from
Apr 7, 2022
Merged

Update centrifuge/centrifuge #1495

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6fa03c8
Fix bug in centrifuge module
sofstam Apr 5, 2022
9ccb1e8
Add centrifuge/centrifuge
sofstam Apr 5, 2022
58d9557
Merge branch 'master' into update_centrifuge
sofstam Apr 5, 2022
42c44ae
Fix index for centrifuge db
sofstam Apr 6, 2022
4190ec8
Update modules/centrifuge/centrifuge/main.nf
sofstam Apr 7, 2022
c418ab8
Update tests/modules/centrifuge/centrifuge/main.nf
sofstam Apr 7, 2022
f8123bb
Merge branch 'master' into centrifuge_centrifuge
sofstam Apr 7, 2022
421a299
Update centrifuge_centrifuge
sofstam Apr 7, 2022
fa2231f
Update meta.yml
sofstam Apr 7, 2022
3f6d358
Update modules/centrifuge/centrifuge/meta.yml
sofstam Apr 7, 2022
181aafd
Update meta.yml
sofstam Apr 7, 2022
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Update modules/centrifuge/centrifuge/main.nf 
Co-authored-by: James A. Fellows Yates <[email protected]>
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@sofstam @jfy133
sofstam and jfy133 authored Apr 7, 2022
commit 4190ec817bbb00675c4ed12a7ab4fcf8f3caa5d5
1 change: 1 addition & 0 deletions modules/centrifuge/centrifuge/main.nf
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Expand Up @@ -41,6 +41,7 @@ process CENTRIFUGE_CENTRIFUGE {
}
def sam_output = sam_format ? "--out-fmt 'sam'" : ''
"""
// we add `-no-name ._` to ensure silly Mac OSX metafiles files aren't included
db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'`
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centrifuge \\
-x \$db_name \\
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