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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c4a7d094c8
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Fix EditorConfig check
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2022-10-28 14:33:44 +02:00 |
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Sofia Stamouli
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5b99d9024a
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Add samtools stats for short-reads
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2022-10-28 14:24:33 +02:00 |
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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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James A. Fellows Yates
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10f7f9e5de
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Merge branch 'adapterremoval-fix' of https://github.com/nf-core/taxprofiler into adapterremoval-fix
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2022-10-27 12:23:52 +00:00 |
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James A. Fellows Yates
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08d61065e5
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Add adapterlist to AR2 subworkflow
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2022-10-27 12:23:27 +00:00 |
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nf-core-bot
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a402ee3be2
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[automated] Fix linting with Prettier
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2022-10-27 12:20:08 +00:00 |
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James A. Fellows Yates
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733d3dc8c5
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Apply suggestions from code review
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2022-10-27 14:19:28 +02:00 |
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James A. Fellows Yates
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76a662ecc5
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Fix adapterremoval adapter conflict and add optional adapter list file
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2022-10-27 12:17:19 +00:00 |
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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 |
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Sofia Stamouli
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d3d4297ca9
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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
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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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Moritz E. Beber
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c7c7a7f678
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refactor: change Bracken prefix to be more specific
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2022-10-19 16:20:09 +02:00 |
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Sofia Stamouli
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7881ba9aef
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Fix the amount of left-padding spaces
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2022-10-18 17:50:49 +02:00 |
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Sofia Stamouli
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0481bb9449
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Prettier
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2022-10-18 17:48:40 +02:00 |
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Sofia Stamouli
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8eddb32b88
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Add Falco as an alternative to FastQC
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2022-10-18 17:43:16 +02:00 |
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Moritz E. Beber
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8768a16d63
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refactor: turn warning into error
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2022-10-17 17:35:41 +02:00 |
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Moritz E. Beber
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48b00b7d62
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refactor: create standardized Bracken reports
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2022-10-17 17:33:24 +02:00 |
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Moritz E. Beber
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fd8a0df2a6
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refactor: add warning when run_kraken2 is missing
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2022-10-17 17:16:21 +02:00 |
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Moritz E. Beber
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563b34c9c3
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refactor: rename process to kraken2
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2022-10-14 14:48:27 +02:00 |
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Moritz E. Beber
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95621ebd8a
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fix: include local module
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2022-10-14 14:47:08 +02:00 |
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James A. Fellows Yates
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4f27998852
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Update usage.md
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2022-10-14 14:37:52 +02:00 |
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Moritz E. Beber
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9dc819ceff
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style: reformat schema
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2022-10-14 13:16:54 +02:00 |
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Moritz E. Beber
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c4f6468275
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chore: update parameters schema
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2022-10-14 12:55:26 +02:00 |
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Moritz E. Beber
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7f8180f458
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fix: emit tool versions
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2022-10-14 12:49:07 +02:00 |
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Moritz E. Beber
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767663d975
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chore: add Bracken to test configs
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2022-10-14 12:18:55 +02:00 |
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Moritz E. Beber
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ca38d002de
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feat: integrate Bracken into the profiling pipeline
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2022-10-14 12:18:07 +02:00 |
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Moritz E. Beber
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4f728648f5
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feat: add process to standardize kraken report
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2022-10-14 10:56:14 +02:00 |
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Moritz E. Beber
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4352d35937
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chore: install Bracken module
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2022-10-14 10:52:17 +02:00 |
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Sofia Stamouli
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4e771ab2c7
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Merge pull request #142 from genomic-medicine-sweden/update_readme
Add KrakenUniq and Filtlong in documentation
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2022-10-12 11:38:01 +02:00 |
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Sofia Stamouli
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bd56bc0ed6
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Add minimap2 and update contributors
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2022-10-12 11:10:53 +02:00 |
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