Moritz E. Beber
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a425a322f2
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refactor: make metaphlan3 run in workflow
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2022-04-02 14:59:44 +02:00 |
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Moritz E. Beber
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69db920610
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feat: include metaphlan3 in workflow
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2022-04-02 14:59:44 +02:00 |
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Moritz E. Beber
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4d2960c06f
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chore: add metaphlan3 module
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2022-04-02 14:59:44 +02:00 |
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James A. Fellows Yates
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1dfbcacf68
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Merge pull request #34 from nf-core/adapterremoval
Add AdapterRemoval as alternative trimer/merger
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2022-04-02 10:33:45 +02:00 |
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James Fellows Yates
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93aaa9eeac
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Clean up AdapterRemoval and remove all debugging dumps
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2022-04-01 21:36:22 +02:00 |
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James A. Fellows Yates
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03e832954f
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Update subworkflows/local/shortread_adapterremoval.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-04-01 20:55:33 +02:00 |
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James A. Fellows Yates
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14f2b7bd84
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-04-01 15:34:05 +02:00 |
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James Fellows Yates
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0d0b377dfb
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Add additional test
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2022-04-01 11:19:00 +02:00 |
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James Fellows Yates
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df4f13319f
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More linting
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2022-04-01 11:13:57 +02:00 |
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James Fellows Yates
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b04cfec2c2
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Prettier linting
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2022-04-01 11:13:36 +02:00 |
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James Fellows Yates
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dcda815bfb
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Add final adapterremoval options to match fastp functionality
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2022-04-01 09:50:08 +02:00 |
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James Fellows Yates
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c4c93bd59d
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Start working on adding adapterremoval
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2022-03-31 15:31:45 +02:00 |
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James A. Fellows Yates
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323883bd3e
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Merge pull request #33 from nf-core/improve-shortread-input
Improve shortread input preprocessing
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2022-03-30 11:48:32 +02:00 |
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James Fellows Yates
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76e9624e3f
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NOW commit the adapte rtrim flag
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2022-03-30 11:31:37 +02:00 |
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James Fellows Yates
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98a9688329
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Change CPUs back to template, update skiptrim fiag
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2022-03-29 15:18:06 +02:00 |
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Sofia Stamouli
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c552819c72
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Apply prettier again
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2022-03-28 22:15:31 +02:00 |
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sofstam
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d25f97c506
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Prettier format
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2022-03-28 22:08:05 +02:00 |
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James Fellows Yates
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04fb6f4127
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Use new resources for test data
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2022-03-28 20:38:16 +02:00 |
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James Fellows Yates
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94e5cfef4a
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Filter long reads for MALT, bump cpus for FastQC for minigut to pass
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2022-03-28 18:20:10 +02:00 |
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James Fellows Yates
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eada201eb2
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Prettier
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2022-03-28 16:47:37 +02:00 |
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James Fellows Yates
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98dc8014a5
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Fix kraken2 module
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2022-03-28 16:46:45 +02:00 |
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James Fellows Yates
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231253227c
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Remove run merging for now due to complexity
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2022-03-28 16:38:10 +02:00 |
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sofstam
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0e0e8128e8
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Prettier format
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2022-03-28 13:53:16 +02:00 |
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James Fellows Yates
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ee53283696
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Debugging comment
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2022-03-28 09:13:05 +02:00 |
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James Fellows Yates
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8dc9e583ad
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Debugging run merging
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2022-03-27 09:30:23 +02:00 |
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James A. Fellows Yates
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e6e8ed7cc9
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Add some debugging notes
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2022-03-26 20:54:50 +00:00 |
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James A. Fellows Yates
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622fafedc8
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Prempt centrifuge database untar crash
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2022-03-26 20:22:35 +00:00 |
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James Fellows Yates
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120382f51d
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Fix input channels to kraken2
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2022-03-26 06:45:16 +01:00 |
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sofstam
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59d3f18a75
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Update nextflow_schema.json
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2022-03-25 17:18:04 +01:00 |
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sofstam
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16bdc79cc0
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Apply prettier
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2022-03-25 16:30:26 +01:00 |
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sofstam
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37a70dc3e3
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Merge branch 'dev' into classification_centrifuge
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2022-03-25 16:18:35 +01:00 |
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James A. Fellows Yates
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000f129dab
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Apply suggestions from code review
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2022-03-25 15:32:56 +01:00 |
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James Fellows Yates
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ede362dbf9
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Remove duplicate config and sync longread fastqc
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2022-03-25 15:28:30 +01:00 |
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James Fellows Yates
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b763bfa2c0
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More cleanup
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2022-03-25 15:26:57 +01:00 |
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James Fellows Yates
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0e6f7e2ca1
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Revert "Some more cleanup"
This reverts commit 7ddcb09a85 .
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2022-03-25 15:24:10 +01:00 |
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James Fellows Yates
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7ddcb09a85
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Some more cleanup
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2022-03-25 15:22:41 +01:00 |
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James Fellows Yates
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b5f5c75504
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Fix file header descriptions
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2022-03-25 15:21:52 +01:00 |
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James Fellows Yates
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dfcf8f7b1a
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Prettier
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2022-03-25 15:10:52 +01:00 |
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James Fellows Yates
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ff1f28f4f0
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Update schema
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2022-03-25 15:01:25 +01:00 |
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James Fellows Yates
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4e93abc7c0
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Add read improved read preprocessing
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2022-03-25 14:58:06 +01:00 |
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James A. Fellows Yates
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fafb7e0f6f
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Update README.md
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2022-03-24 16:59:12 +01:00 |
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James A. Fellows Yates
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f3c21203c8
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Merge pull request #32 from nf-core/nf-core-template-merge-2.3.2
Important! Template update for nf-core/tools v2.3.2
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2022-03-24 15:50:38 +01:00 |
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James Fellows Yates
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92a3c8ec8d
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Prettier
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2022-03-24 15:40:14 +01:00 |
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James Fellows Yates
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494c641fb8
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Prettier
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2022-03-24 15:37:42 +01:00 |
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James Fellows Yates
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cc9368ee52
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Prettier linting and update schema
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2022-03-24 15:35:09 +01:00 |
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James Fellows Yates
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203cd2e7d3
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Prettier
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2022-03-24 14:31:53 +01:00 |
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James Fellows Yates
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e3be393f16
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Fix broken json
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2022-03-24 14:18:15 +01:00 |
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James A. Fellows Yates
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edce6603ef
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Merge branch 'dev' into nf-core-template-merge-2.3.2
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2022-03-24 14:10:58 +01:00 |
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sofstam
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3ff54e620e
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Add centrifuge classification
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2022-03-24 13:02:25 +01:00 |
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nf-core-bot
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feeb8ba8dd
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Template update for nf-core/tools version 2.3.2
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2022-03-24 11:48:43 +00:00 |
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