James A. Fellows Yates
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770a35d7ac
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Update conf/modules.config
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2022-11-29 12:49:20 +01:00 |
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Sofia Stamouli
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ba727a81ae
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Fix left-padding spaces
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2022-11-29 12:45:14 +01:00 |
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Sofia Stamouli
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71b52b9c94
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Apply review suggestions
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2022-11-29 11:58:23 +01:00 |
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James A. Fellows Yates
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3d949a803f
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Merge pull request #175 from nf-core/schema-clean
Fix schema location ofr fastqc/falco option
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2022-11-29 11:49:27 +01:00 |
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Sofia Stamouli
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fb6be69d7e
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Prettier should work now
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2022-11-29 11:37:20 +01:00 |
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sofstam
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644a29c699
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Prettier
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2022-11-29 11:34:57 +01:00 |
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sofstam
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5254b8d679
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Prettier
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2022-11-29 11:25:52 +01:00 |
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sofstam
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0235ef42ca
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Update nextflow_schema.json
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2022-11-29 11:15:40 +01:00 |
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sofstam
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49af33f68e
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Include NCBI_id, read counts and mgc arguments in motus
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2022-11-29 11:07:29 +01:00 |
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Moritz E. Beber
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af8ce2cbfd
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chore: update krakenuniq
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2022-11-29 10:27:35 +01:00 |
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James Fellows Yates
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d6c0ebb4c6
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Prettier
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2022-11-29 10:14:33 +01:00 |
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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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f13185d98b
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Fix schema location ofr fastqc/falco option
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2022-11-29 10:13:46 +01:00 |
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James A. Fellows Yates
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f114cc4122
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Apply suggestions from code review
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2022-11-24 16:55:19 +01:00 |
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James A. Fellows Yates
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17b1e3df1c
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Update test.config
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2022-11-24 16:53:39 +01:00 |
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James Fellows Yates
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a20b3e3c58
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Try to reduce MALT memory
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2022-11-24 15:51:12 +01:00 |
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James Fellows Yates
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131b39aa8b
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Fix linting
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2022-11-24 15:49:06 +01:00 |
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James Fellows Yates
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9feb6c2db6
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Update MALT
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2022-11-24 14:44:04 +01:00 |
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Sofia Stamouli
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f8b769a8f0
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Merge pull request #172 from genomic-medicine-sweden/update_samtools_stats
Include the mapped reads in samtools stats
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2022-11-23 10:21:47 +01:00 |
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sofstam
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481f90589c
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Apply review suggestions
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2022-11-23 09:08:22 +01:00 |
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Moritz E. Beber
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b6f5930b49
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Merge pull request #171 from nf-core/chore-fail-slow
chore: let all tests run to completion
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2022-11-22 19:22:14 +01:00 |
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sofstam
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30af26a8b3
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Include the mapped reads in samtools stats
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2022-11-22 16:50:50 +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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Moritz E. Beber
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6b538d658a
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chore: let all tests run to completion
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2022-11-22 10:13:10 +01:00 |
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James A. Fellows Yates
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10c72f1265
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Merge pull request #169 from nf-core/diagram-update
Update tubemap to include samtools stats
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2022-11-06 10:15:56 +01:00 |
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James Fellows Yates
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f414f5dc9c
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Add falco to tube map
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2022-11-04 18:20:44 +01:00 |
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James Fellows Yates
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4275640d9b
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update tubemap to include samtools stats
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2022-11-04 15:24:15 +01:00 |
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James A. Fellows Yates
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67e264b7a9
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Merge pull request #162 from genomic-medicine-sweden/short_reads_samtools
Add samtools stats for short-reads
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2022-11-04 14:39:29 +01:00 |
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Sofia Stamouli
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696edfb866
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Apply prettier
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2022-11-04 12:05:23 +01:00 |
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Sofia Stamouli
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d2195e9eda
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Merge branch 'dev' into short_reads_samtools
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2022-11-04 11:47:36 +01:00 |
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Sofia Stamouli
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79dd3930bb
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Add samtools to README
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2022-11-03 16:52:01 +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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Sofia Stamouli
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b5e6639f9d
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Apply review suggestions
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2022-11-03 14:12:05 +01:00 |
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