James A. Fellows Yates
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ebdd5683b2
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Apply suggestions from code review
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2022-06-03 22:33:48 +02:00 |
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James Fellows Yates
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9462032d00
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Fix MALT save_alignemnts reads and some clean up
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2022-06-03 22:29:04 +02:00 |
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James A. Fellows Yates
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96fecb2bfc
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Merge branch 'dev' into support-aligned-reads
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2022-06-03 13:48:54 +02:00 |
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James A. Fellows Yates
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c9581b1796
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Merge branch 'dev' into support-aligned-reads
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2022-06-02 12:45:29 +02:00 |
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James Fellows Yates
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310ac6b450
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Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong
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2022-05-31 13:05:52 +02:00 |
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James Fellows Yates
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47a5ae0cff
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Add FASTP complexity option
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2022-05-07 06:09:05 +02:00 |
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James Fellows Yates
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87a1d80519
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Add working output for Kraken2/Centrifuge/DIAMOND
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2022-05-07 05:22:35 +02:00 |
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James A. Fellows Yates
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e7b54801ed
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Merge pull request #75 from nf-core/improve-error-message
Only create profiler input channels when profiler activated
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2022-05-06 11:51:33 +02:00 |
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ljmesi
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5e6be52fab
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Implement hostremoval
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2022-05-03 09:34:27 +02:00 |
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James Fellows Yates
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d5049a34e4
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Add missing close bracket
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2022-05-01 07:28:29 +02:00 |
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James Fellows Yates
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4094706421
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Only create profiler input channels when profiler activate
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2022-05-01 07:24:58 +02:00 |
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James Fellows Yates
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031cb45934
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Add initial longread QC filtering - requires filtlong module update
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2022-05-01 07:18:14 +02:00 |
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James Fellows Yates
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8126d16dee
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Add draft version of DIAMOND
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2022-04-29 21:59:42 +02:00 |
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sofstam
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d082d67bcb
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Add kaiju2table to taxprofiler
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2022-04-25 17:36:29 +02:00 |
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James A. Fellows Yates
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bc84afe80d
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Merge pull request #66 from nf-core/versions-fix
Fix version reporting
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2022-04-25 16:38:28 +02:00 |
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James Fellows Yates
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06b38f3699
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Fix crash, add missing versions
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2022-04-23 08:36:01 +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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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 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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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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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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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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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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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 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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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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James Fellows Yates
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9f221f84cc
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Only supply single input channel to profiling, as these are merged into single input channel at run_merging
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2022-04-12 10:12:17 +02:00 |
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James A. Fellows Yates
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967b1f7d6e
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Merge branch 'dev' into run-merging
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2022-04-12 09:28:10 +02:00 |
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James A. Fellows Yates
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025083061e
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Merge branch 'dev' into hostremoval
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2022-04-11 13:36:03 +02:00 |
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James Fellows Yates
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030099c559
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A bit of clean up
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2022-04-10 07:26:20 +02:00 |
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James Fellows Yates
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ecf0eea4f9
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Move profiling to subworkflow and standardise outputs
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2022-04-10 06:43:30 +02:00 |
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James Fellows Yates
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35cb6e042a
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Flatten the right thing
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2022-04-08 13:46:12 +02:00 |
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James Fellows Yates
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6c14f2b230
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Remove the flattening?
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2022-04-08 13:44:52 +02:00 |
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James Fellows Yates
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a634814d84
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Formatting and fix fastp output
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2022-04-08 13:34:00 +02:00 |
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James Fellows Yates
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d130a72d74
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Get this working
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2022-04-08 13:09:23 +02:00 |
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sofstam
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606e5da7d5
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Check if PR works with centrifuge/centrifuge module
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2022-04-07 16:13:17 +02:00 |
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James A. Fellows Yates
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b554aa3e4d
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Merge branch 'dev' into hostremoval
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2022-04-07 14:00:10 +02:00 |
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