Moritz E. Beber
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ddcf38de22
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refactor: make mappings explicit
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2022-11-29 10:14:20 +01:00 |
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James Fellows Yates
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a383c9ae40
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Remove the join
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2022-11-22 13:39:21 +01:00 |
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James Fellows Yates
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06659af777
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Remove flatten
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2022-11-22 13:36:40 +01:00 |
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James Fellows Yates
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cacd7d3128
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Not just in stub
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2022-11-22 13:33:13 +01:00 |
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James Fellows Yates
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e8de006ed6
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With a join
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2022-11-22 13:27:49 +01:00 |
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James Fellows Yates
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ebfc84e235
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Does the grouping work if we have meta?
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2022-11-22 13:26:54 +01:00 |
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James Fellows Yates
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21759807f7
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Does flatten work?
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2022-11-22 12:48:54 +01:00 |
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James Fellows Yates
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3102e40052
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dump teh db
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2022-11-22 12:46:26 +01:00 |
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James Fellows Yates
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557f2a4d96
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Extra dump
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2022-11-22 12:26:46 +01:00 |
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James Fellows Yates
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5caebcc6ab
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Append to correct db
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2022-11-22 12:21:59 +01:00 |
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James Fellows Yates
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52fc00802b
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Correct meta name for db meta
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2022-11-22 12:19:56 +01:00 |
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James Fellows Yates
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b8937748d3
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Fix meta.id isssue
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2022-11-22 12:18:52 +01:00 |
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James Fellows Yates
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db334c5185
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Fix missing info
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2022-11-22 12:17:08 +01:00 |
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James Fellows Yates
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0f298dca43
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group krakenuniq reads by pairs or single end
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2022-11-22 12:13:08 +01:00 |
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James Fellows Yates
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461482d22a
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Try again wit hthe corret param
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2022-11-03 15:02:22 +01:00 |
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James Fellows Yates
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93f38b14a8
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Save report
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2022-11-03 15:01:00 +01:00 |
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James Fellows Yates
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c5e5696f84
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Fix parameter name
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2022-11-03 14:58:03 +01:00 |
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James Fellows Yates
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c03a21c770
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Merge branch 'add-krakenuniq-module' of github.com:mjamy/taxprofiler into add-krakenuniq-module
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2022-11-03 14:56:43 +01:00 |
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James Fellows Yates
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21a76c2449
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Fix cardinality issue
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2022-11-03 14:56:26 +01:00 |
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nf-core-bot
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0c445759e4
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[automated] Fix linting with Prettier
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2022-11-03 13:42:39 +00:00 |
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James Fellows Yates
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6459d8920f
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Linting!
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2022-11-03 14:05:43 +01:00 |
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Mahwash Jamy
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aecf308840
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Update documentation for krakenuniq
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2022-10-31 16:41:35 +00:00 |
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Mahwash Jamy
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851016e497
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Update nextflow_scheme.json
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2022-10-31 16:17:40 +00:00 |
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Mahwash Jamy
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febcbfc057
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add missing parameters to nextflow.config
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2022-10-31 16:07:53 +00:00 |
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Mahwash Jamy
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3147a80a56
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Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module
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2022-10-31 15:36:57 +00:00 |
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Sofia Stamouli
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074d3ec204
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Merge pull request #161 from genomic-medicine-sweden/samtools_stats
Add samtools stats for long-reads
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2022-10-31 10:59:37 +01:00 |
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Sofia Stamouli
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f1778acf35
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Apply review suggestion
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2022-10-31 09:31:13 +01:00 |
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Sofia Stamouli
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f87131c7b1
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Save samtools stats output
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2022-10-28 14:10:24 +02:00 |
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Sofia Stamouli
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1bd6dbfe58
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Add samtools stats for long-reads
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2022-10-28 11:40:50 +02:00 |
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Moritz E. Beber
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bf89525bc2
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Merge pull request #146 from nf-core/feat-bracken
add Bracken to the profiling workflow
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2022-10-27 17:35:06 +02:00 |
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Moritz E. Beber
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e658fab430
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fix: remove def
No idea why, must have something to do with scope.
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2022-10-27 11:50:47 +02:00 |
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Moritz E. Beber
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dd1a4ff158
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refactor: only combine same database name
[skip ci]
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2022-10-27 11:19:14 +02:00 |
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Moritz E. Beber
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0de1ac5356
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docs: add Bracken reference
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2022-10-27 10:14:57 +02:00 |
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Sofia Stamouli
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63c260bfbc
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Merge pull request #148 from genomic-medicine-sweden/add_falco
Add Falco as an alternative to FastQC
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2022-10-25 12:40:26 +02:00 |
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Mahwash Jamy
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f4717be9ab
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add krakenuniq to modules.config
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2022-10-25 09:50:44 +00:00 |
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Mahwash Jamy
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86ca71cfd4
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include krakenuniq in profiling subworkflow
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2022-10-25 09:45:05 +00:00 |
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Mahwash Jamy
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36e101a78b
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Install krakenuniq module
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2022-10-25 09:26:33 +00:00 |
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Sofia Stamouli
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de6816ec49
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Update nextflow_schema.json
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-10-25 11:19:16 +02:00 |
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Sofia Stamouli
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7b1a53b062
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Update nextflow_schema.json
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-10-25 11:19:08 +02:00 |
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Sofia Stamouli
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8c3e80b6ea
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Add helptest to nextflow_schema,add versions to longread_preprocessing
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2022-10-25 11:13:26 +02:00 |
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nf-core-bot
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00038db634
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[automated] Fix linting with Prettier
|
2022-10-25 08:51:58 +00:00 |
|
Sofia Stamouli
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d3d4297ca9
|
Apply review suggestions
|
2022-10-24 16:28:07 +02:00 |
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Moritz E. Beber
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ca7dc308cb
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Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-10-21 16:36:35 +02:00 |
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Moritz E. Beber
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60e369aa5c
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fix: set default run bracken to false
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2022-10-21 10:47:51 +02:00 |
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Moritz E. Beber
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7bd6112133
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docs: describe Bracken database usage
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2022-10-21 10:18:11 +02:00 |
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Moritz E. Beber
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385507ec6f
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refactor: use tool name 'bracken' only
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2022-10-21 10:03:36 +02:00 |
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Sofia Stamouli
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19231538da
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Prettier
|
2022-10-20 16:59:32 +02:00 |
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Sofia Stamouli
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511cb16a61
|
Apply review suggestions
|
2022-10-20 16:55:57 +02:00 |
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Moritz E. Beber
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8deb7757d8
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fix: remove Bracken from standardise reports
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2022-10-19 16:21:57 +02:00 |
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Moritz E. Beber
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b73b479860
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refactor: handle combined kraken2+bracken tool column
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2022-10-19 16:21:36 +02:00 |
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