Sofia Stamouli
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e7e24c2d95
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Prettier and suggestions from review
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2022-04-25 09:21:29 +02:00 |
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sofstam
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c00ca1c2b8
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Add centrifuge kreport in taxprofiler
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2022-04-22 15:24:10 +02:00 |
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James A. Fellows Yates
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63230c3254
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Merge pull request #63 from nf-core/maxforks
Update test.config to only allow maxFork to 1 for MALT_RUN
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2022-04-21 12:57:37 +02:00 |
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James A. Fellows Yates
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47a34d4c7e
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Merge pull request #59 from nf-core/hostremoval-publish-fix
Add finer control over for hostremoval saving
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2022-04-21 12:57:09 +02:00 |
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James A. Fellows Yates
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cd3c8f6a89
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Merge branch 'dev' into hostremoval-publish-fix
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2022-04-21 11:43:06 +02:00 |
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James A. Fellows Yates
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d850333e11
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Linting
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2022-04-20 13:42:26 +02:00 |
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James A. Fellows Yates
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d031322c16
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Update test.config
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2022-04-20 13:41:01 +02:00 |
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Sofia Stamouli
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e71e7b86a2
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Merge pull request #53 from genomic-medicine-sweden/classification_kaiju
Add kaiju/kaiju in taxprofiler
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2022-04-20 10:57:00 +02:00 |
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Sofia Stamouli
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236141f065
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Resolve conflicts with dev
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2022-04-20 10:17:10 +02:00 |
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James A. Fellows Yates
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571495c812
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Merge pull request #60 from nf-core/fasta-filtering
Adds filtering out of FASTA for tools that don't support it
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2022-04-20 10:11:17 +02:00 |
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James A. Fellows Yates
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d16cd75652
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Merge branch 'dev' into hostremoval-publish-fix
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2022-04-20 09:53:51 +02:00 |
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James A. Fellows Yates
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53d76559af
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Merge pull request #55 from nf-core/megan-postprocessing
Add MEGAN for MALT postprocessing
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2022-04-20 09:52:55 +02:00 |
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James A. Fellows Yates
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fb5347a9fc
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Merge pull request #58 from nf-core/docs
Add documentation for preprocessing subworkflows
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2022-04-20 09:26:53 +02:00 |
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James Fellows Yates
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9fd94b1389
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Switch to string interpolation
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2022-04-20 09:25:54 +02:00 |
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James Fellows Yates
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60d232d62c
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Revert "Update subworkflows/local/profiling.nf"
This reverts commit b7d0557ee0 .
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2022-04-20 09:23:38 +02:00 |
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James A. Fellows Yates
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ac714dd30f
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-04-20 09:22:10 +02:00 |
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James A. Fellows Yates
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b7d0557ee0
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Update subworkflows/local/profiling.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-04-20 09:15:45 +02:00 |
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Sofia Stamouli
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4e1b1269be
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Apply prettier
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2022-04-19 13:11:43 +02:00 |
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Sofia Stamouli
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dc276e8bae
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Merge branch 'nf-core:dev' into classification_kaiju
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2022-04-19 13:09:15 +02:00 |
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sofstam
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1b7ff2265d
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Update usage.md, reformat test.config and modules.config
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2022-04-19 13:04:58 +02:00 |
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James A. Fellows Yates
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87777a4289
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Update subworkflows/local/profiling.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-04-19 12:54:57 +02:00 |
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James A. Fellows Yates
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ecaff371aa
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Update input_check.nf
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2022-04-18 07:35:19 +02:00 |
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James A. Fellows Yates
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9f634805e4
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Update subworkflows/local/profiling.nf
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2022-04-18 07:31:44 +02:00 |
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James A. Fellows Yates
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9c3c8f1f4e
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Merge branch 'dev' into fasta-filtering
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2022-04-18 07:31:14 +02:00 |
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James Fellows Yates
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6307a9cf43
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Typos
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2022-04-18 07:28:09 +02:00 |
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James Fellows Yates
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491c2d8949
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Revert "Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages."
This reverts commit 564474cafe .
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2022-04-18 07:26:15 +02:00 |
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James Fellows Yates
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564474cafe
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Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages.
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2022-04-18 07:21:12 +02:00 |
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James Fellows Yates
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9880baa0b8
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Get build directory working
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2022-04-18 06:37:23 +02:00 |
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James Fellows Yates
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b036ed5b73
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Prettier
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2022-04-17 22:28:18 +02:00 |
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James Fellows Yates
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2cfcdf2dd2
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Add finer controler over for hostremoval saving
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2022-04-17 22:27:04 +02:00 |
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James Fellows Yates
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457c13e8b7
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Add additional tips for host removal
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2022-04-17 17:55:23 +02:00 |
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James Fellows Yates
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818d3bd053
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Complete documentation for preprocessing subworkflows
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2022-04-17 17:53:22 +02:00 |
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James Fellows Yates
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d0256ec937
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Prettier
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2022-04-16 07:45:24 +02:00 |
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James Fellows Yates
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cc73cdd51d
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Add generation of taxon-table like output for MALT
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2022-04-16 07:42:30 +02:00 |
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James A. Fellows Yates
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6fecb3eeb7
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Merge pull request #54 from nf-core/dev
Get upstream changes
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2022-04-16 06:17:33 +02:00 |
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sofstam
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0e5c9e7bdd
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Type:boolean for kaiju in nextflow_schema.json
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2022-04-14 09:14:05 +02:00 |
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sofstam
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6736a2a980
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Update README.md, nextflow_schema.json
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2022-04-13 19:00:52 +02:00 |
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sofstam
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68ce5843a4
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Add kaiju in taxprofiler
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2022-04-13 18:51:56 +02:00 |
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James A. Fellows Yates
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fc8a83245a
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Add short-read host removal via BowTie2 alignment mapping
Add short-read host removal via BowTie2 alignment mapping
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2022-04-13 15:29:16 +02:00 |
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James A. Fellows Yates
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5e80df0f94
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Apply suggestions from code review
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2022-04-13 15:27:53 +02:00 |
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James Fellows Yates
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aa2d07c42a
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Fix merge cockup
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2022-04-13 14:19:19 +02:00 |
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James A. Fellows Yates
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70f94603b0
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Merge branch 'dev' into hostremoval
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2022-04-13 13:59:51 +02:00 |
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James A. Fellows Yates
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67d94a9a8d
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Merge pull request #45 from nf-core/run-merging
Re-add run merging
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2022-04-13 12:27:37 +02:00 |
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James Fellows Yates
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dfeaa0d1fe
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Rename subworkflow parameters for consistency
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2022-04-13 12:00:28 +02:00 |
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James Fellows Yates
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de57340526
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Start work
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2022-04-13 11:49:35 +02:00 |
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James Fellows Yates
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16a3556bfc
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Changes after code review
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2022-04-13 08:26:08 +02:00 |
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James Fellows Yates
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a15c45b00c
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Put map in the rigt place
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2022-04-12 10:51:27 +02:00 |
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James Fellows Yates
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8d68914192
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Re-add operator name
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2022-04-12 10:47:44 +02:00 |
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James Fellows Yates
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26399718b2
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Re-add pairment attachment
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2022-04-12 10:46:03 +02:00 |
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James Fellows Yates
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2ef21c6ef3
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Fix input to profiling
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2022-04-12 10:14:05 +02:00 |
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