James A. Fellows Yates
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2cbb56194a
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Merge pull request #224 from nf-core/revert-metaphlan-nanopore-filter [skip ci]
Remove metaphlan3 nanopore filter as _sometimes_ it can work
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2023-01-25 13:48:29 +01:00 |
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James A. Fellows Yates
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098ec087c9
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Merge pull request #217 from nf-core/combine-kreports-fix [skip ci]
Dont fail on divide by 0 errors on centrifuge
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2023-01-25 13:48:06 +01:00 |
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James A. Fellows Yates
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4289e1f901
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Remove metaphlan3 nanopore filter as _sometimes_ it can work
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2023-01-24 15:42:14 +01:00 |
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Moritz E. Beber
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2431bddcbc
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Merge pull request #222 from nf-core/fix-save-minimap2
fix: correct pattern to publish minimap2 index
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2023-01-24 14:57:46 +01:00 |
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James A. Fellows Yates
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00178d3431
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Merge pull request #221 from nf-core/metaphlan3-filter-nanopore
Filter out nanopore data prior Metaphlan3
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2023-01-24 14:39:02 +01:00 |
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Moritz E. Beber
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40f1e7b27a
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fix: correct pattern to publish minimap2 index
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2023-01-24 14:15:51 +01:00 |
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James Fellows Yates
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14826d5205
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Separate conditions, remove some left-over dumps
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2023-01-24 13:20:58 +01:00 |
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James Fellows Yates
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0358489be0
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Remove metaphlan profiling for nanopore as it appears to always result in 100% unclassified
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2023-01-24 13:05:52 +01:00 |
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James A. Fellows Yates
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38cbfe9a1c
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Merge pull request #220 from nf-core/sr-lr-guidance
Add comment about recommendation to split SR/LR
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2023-01-24 11:51:18 +01:00 |
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James A. Fellows Yates
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9cf2d8763f
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[skip ci] Update docs/usage.md
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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2023-01-24 11:50:58 +01:00 |
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James Fellows Yates
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9205831273
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Start adding filter for long read and MP3
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2023-01-24 11:50:10 +01:00 |
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James A. Fellows Yates
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03ef6a69f8
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Merge pull request #215 from nf-core/remove-platform-specificity
Remove platform specificity for MALT
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2023-01-24 11:47:48 +01:00 |
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James Fellows Yates
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085d9e519c
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[skip ci] add comment about recommendation to split SR/LR
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2023-01-24 11:39:37 +01:00 |
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James Fellows Yates
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2439aa69d0
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Use specific samplesheet for MALT without LR reads due to GHA memory limits
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2023-01-24 10:58:03 +01:00 |
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James Fellows Yates
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1c820f21b3
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Dont fail on divide by 0 errors on centrifuge
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2023-01-20 17:53:55 +01:00 |
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James A. Fellows Yates
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d3bad1d720
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Merge pull request #214 from nf-core/local-module-template-sync
Sync local modules with latest template module structure
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2023-01-20 14:41:11 +01:00 |
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James Fellows Yates
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606ffc0eb1
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Remove platform specificity for MALT
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2023-01-20 13:40:59 +01:00 |
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James Fellows Yates
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cac6f54d2d
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[extra] Fix warn related to recently changed parameter
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2023-01-20 13:36:17 +01:00 |
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James Fellows Yates
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2d64628552
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Fix left-over warns from loca modules
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2023-01-20 13:33:43 +01:00 |
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James A. Fellows Yates
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d9003924be
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Merge pull request #201 from genomic-medicine-sweden/removo_todo
Remove TODOs from test configs
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2023-01-19 13:15:14 +01:00 |
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James A. Fellows Yates
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5162240e77
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Merge pull request #208 from nf-core/post-usage-draft-tweaks
Post-release tweaks to usage.md
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2023-01-19 11:09:54 +01:00 |
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James A. Fellows Yates
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36629b3dde
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Merge branch 'dev' into post-usage-draft-tweaks
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2023-01-19 10:36:59 +01:00 |
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James A. Fellows Yates
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49e4e20f84
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Merge pull request #212 from nf-core/classification-v-profiling
Specify the difference between classification/profiling
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2023-01-19 10:06:15 +01:00 |
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James A. Fellows Yates
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6e43695264
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Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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2023-01-19 08:55:23 +01:00 |
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James A. Fellows Yates
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6d380fbbff
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Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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2023-01-19 08:49:55 +01:00 |
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James Fellows Yates
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33d4a84237
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Add explicit sentnece about classification/profiling
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2023-01-17 15:23:59 +01:00 |
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James A. Fellows Yates
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0cda0d2c51
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Merge pull request #213 from nf-core/multiqc-update
Updates MultiQC to 1.14 to add support for all our MQC modules!
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2023-01-17 13:37:44 +01:00 |
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James Fellows Yates
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92dff9b453
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Standardise file names using only underscore
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2023-01-17 10:58:30 +01:00 |
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James Fellows Yates
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480248bcfd
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Deactivate all classifer columns from general stats
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2023-01-17 10:33:35 +01:00 |
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nf-core-bot
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11400b016c
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[automated] Fix linting with Prettier
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2023-01-16 14:11:18 +00:00 |
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James Fellows Yates
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0947e9b8ca
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Fix mOTUs issues
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2023-01-16 15:09:30 +01:00 |
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James Fellows Yates
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c8f6d713a3
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Add tool names to end of prefix files for easier distinguishing in general stats
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2023-01-16 14:49:44 +01:00 |
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James A. Fellows Yates
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b34a021db7
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Specify the difference between classification/profiling
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2023-01-16 14:43:46 +01:00 |
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James Fellows Yates
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d6fa45b500
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update MultiQC and include latest modules
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2023-01-16 14:39:52 +01:00 |
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James A. Fellows Yates
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6dcf619518
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Merge pull request #209 from nf-core/module-version-bumps
Update all modules to make templaite compatible
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2022-12-23 23:17:17 +01:00 |
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James Fellows Yates
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e5c6db96c8
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update all modules to make templaite compatible
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2022-12-23 17:23:05 +01:00 |
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James Fellows Yates
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ab0c62bdc1
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Post-release tweaks to usage.md
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2022-12-23 16:23:29 +01:00 |
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James A. Fellows Yates
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75a95d5ed8
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Merge pull request #143 from genomic-medicine-sweden/update_usage
Update usage.md
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2022-12-23 15:14:12 +01:00 |
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James A. Fellows Yates
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acba31a8d6
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Update taxprofiler.nf
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2022-12-23 15:08:01 +01:00 |
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James A. Fellows Yates
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e586747680
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Add missing comma to list
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2022-12-23 15:06:26 +01:00 |
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James A. Fellows Yates
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2de049399d
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Merge pull request #206 from genomic-medicine-sweden/path_params
Add path parameters
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2022-12-23 15:05:59 +01:00 |
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sofstam
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6ebfdcd017
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Add path parameters
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2022-12-23 13:40:22 +01:00 |
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Sofia Stamouli
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59fd676ab3
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Merge pull request #205 from genomic-medicine-sweden/optional_untar
Optional untar on dbs
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2022-12-23 13:14:04 +01:00 |
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Sofia Stamouli
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41c1ae9d1a
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Commit suggestion
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-12-23 12:20:37 +01:00 |
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sofstam
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85906ab1cb
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Optional untar on dbs
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2022-12-23 11:25:57 +01:00 |
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Sofia Stamouli
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ec9c7cfedc
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Prettier
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2022-12-22 11:10:54 +01:00 |
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Sofia Stamouli
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2f291731c1
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Merge branch 'nf-core:dev' into update_usage
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2022-12-22 11:09:50 +01:00 |
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Sofia Stamouli
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1eeb3b337a
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Update usage.md
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2022-12-22 11:07:09 +01:00 |
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Sofia Stamouli
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29978d83b9
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Update centrifuge section
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2022-12-22 11:03:49 +01:00 |
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Sofia Stamouli
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d6e0d404e3
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Update docs/usage.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-12-22 09:18:00 +01:00 |
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