James A. Fellows Yates
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f47c294931
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Merge pull request #186 from genomic-medicine-sweden/update_output
Start the documentation of output.md
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2023-01-31 09:58:54 +01:00 |
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sofstam
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366745bdbe
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Prettier in usage
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2023-01-31 09:38:43 +01:00 |
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sofstam
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5b738ad353
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Review + prettier
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2023-01-31 09:35:40 +01:00 |
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James A. Fellows Yates
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1d7da61801
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Merge pull request #223 from nf-core/multiqc-tweaks
MultiQC Tweaks after full-test experiments
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2023-01-30 11:25:28 +01:00 |
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sofstam
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0edef9ea57
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Review suggestions + prettier
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2023-01-30 11:16:18 +01:00 |
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sofstam
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bc2876228c
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Apply review suggestions
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2023-01-25 15:11:43 +01:00 |
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James Fellows Yates
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a77a437313
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Triple patch combo!
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2023-01-25 15:02:02 +01:00 |
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James Fellows Yates
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f63cec3473
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Actually patch the patch
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2023-01-25 14:58:19 +01:00 |
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James Fellows Yates
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d761edb615
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Patch the patch
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2023-01-25 14:55:57 +01:00 |
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James A. Fellows Yates
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47efd193cb
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Merge pull request #219 from nf-core/allow-targz-motus [skip ci]
Allow all tool's databases to be provided as `.tar.gz` files
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2023-01-25 13:48:43 +01:00 |
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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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sofstam
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4f8ac72e1f
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Add description of each tool
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2023-01-25 13:25:33 +01:00 |
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Sofia Stamouli
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5d12785ca4
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Merge branch 'nf-core:dev' into update_output
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2023-01-25 09:47:30 +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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James Fellows Yates
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7843665544
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Link rather than mv
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2023-01-24 15:32:49 +01:00 |
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James A. Fellows Yates
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c765b3f0bc
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Merge branch 'dev' into allow-targz-motus
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2023-01-24 15:20:29 +01:00 |
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James Fellows Yates
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f940b07dfe
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Remove changes from other PR
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2023-01-24 15:15:02 +01:00 |
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James Fellows Yates
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bdbb111344
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Turn off all profilers in generla stats
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2023-01-24 15:08:28 +01:00 |
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James Fellows Yates
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a993300099
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Tweaks to MultiQC based on full test experiments
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2023-01-24 15:06:42 +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 Fellows Yates
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e7d7affcd0
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Pick up Kraken2 files correctly
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2023-01-24 14:44:14 +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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6eafcc6499
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Try Moritz's trick, assuming validate_db_rows already checks for tool name validity
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2023-01-24 12:43:34 +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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4df3409f4a
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Merge branch 'dev' of github.com:nf-core/taxprofiler into allow-targz-motus
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2023-01-24 11:50:28 +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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1a148c5d49
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Remove double If and format for readability
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2023-01-24 10:48:23 +01:00 |
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James A. Fellows Yates
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d56e3133f9
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Allow databases of all tools to arrive as tar.gz
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2023-01-24 10:45:01 +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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Sofia Stamouli
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7d4035d4c7
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Add new line in the description of custom file
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2023-01-19 13:44:10 +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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Sofia Stamouli
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4dcf8c0b02
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Prettier
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2023-01-17 15:50:10 +01:00 |
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sofstam
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024b683671
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Update output and usage
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2023-01-17 15:38:56 +01:00 |
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