Rafal Stepien
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768f9980d8
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Add pep_input_base_dir to workflow. Just need to update modules
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2022-09-15 12:31:49 -04:00 |
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Rafal Stepien
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5f3eee9a4a
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Add working version of PEP-nf-core integration
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2022-09-14 14:28:48 -04:00 |
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James A. Fellows Yates
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cc5df924e4
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Merge branch 'dev' into module-update
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2022-09-08 13:36:21 +02:00 |
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James Fellows Yates
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fc26948950
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Fix MultiQC
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2022-09-08 12:49:38 +02:00 |
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James Fellows Yates
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d11257b330
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Module update
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2022-09-08 08:08:36 +02:00 |
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James Fellows Yates
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bbd8049ca1
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Remove duplicated multqic mixing
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2022-09-07 13:44:08 +02:00 |
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James Fellows Yates
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7c5f9d0c24
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Start work on more merging tools
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2022-09-06 17:34:45 +02:00 |
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James Fellows Yates
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5552c264b9
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Remove now unnecessary input validation
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2022-08-30 14:14:01 +02:00 |
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James Fellows Yates
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8917e29e35
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Fix accidental overly zelous search-and-replace
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2022-08-30 14:11:48 +02:00 |
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James Fellows Yates
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3f8f32cba8
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Make longread quality ftilering opt out
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2022-08-30 14:08:05 +02:00 |
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James Fellows Yates
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2cc07183a0
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Standardise QC parameter system and turn on both porechop/filtlong in tests
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2022-08-30 13:58:58 +02:00 |
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James Fellows Yates
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139cf0d6aa
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Fix
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2022-07-26 10:12:33 +02:00 |
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James A. Fellows Yates
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cc3967a3fd
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Apply suggestions from code review
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2022-07-15 10:51:41 +02:00 |
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James Fellows Yates
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a0ee82bf43
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Add motus/merge and biom support
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2022-07-12 11:39:26 +02:00 |
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James Fellows Yates
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02c06b9f7b
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Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file
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2022-06-30 18:33:11 +02:00 |
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4de43040a3
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Switch to using raw classifications for Kaiju2Krona
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2022-06-28 09:00:41 -05:00 |
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821dd844d8
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Add Kaiju profile conversion to visualization workflow
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2022-06-27 09:23:20 -05:00 |
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18284e6e32
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Add run_krona option to allow skipping Krona chart creation
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2022-06-27 08:45:08 -05:00 |
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ad9bc4b7e9
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Add the visualization workflow to the main workflow
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2022-06-27 08:25:38 -05:00 |
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James Fellows Yates
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d48b3be5a7
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Tweak DIAMOND save_reads message
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2022-06-03 13:55:17 +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 A. Fellows Yates
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a196e0f628
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Merge branch 'dev' into add-filtlong
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2022-06-02 11:51:26 +02:00 |
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James Fellows Yates
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16ec5bf74a
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Update parameter names
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2022-05-31 20:11:19 +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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77da358e87
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Separate dark and light mode logos, add to README and add to MQC report
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2022-05-31 12:45:38 +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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Lauri Mesilaakso
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b0faeedc60
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Update workflows/taxprofiler.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-05-06 08:20:31 +02:00 |
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ljmesi
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e3e55f57c2
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Fix alignment
Just made this change to see if the CI tests would fail again or if the
failure was just a one of thing.
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2022-05-05 14:02:24 +02:00 |
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ljmesi
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6618e8cac6
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Change param to a more generic name
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2022-05-05 13:20:34 +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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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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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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James Fellows Yates
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cda1274918
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Moves ordering of modules/subworkflow versions mixing to before custom_dumpsoftwareversions mix, otherwise not used in collectFile
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2022-04-23 06:47:59 +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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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 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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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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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 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 Fellows Yates
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a5f4fc42d5
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Fix run merging for unmerged PE data
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2022-04-12 09:25:27 +02:00 |
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James Fellows Yates
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78182c2a8c
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Add comma
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2022-04-11 13:40:24 +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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80c08af11b
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Mix in profiling versions into mainline versons channel
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2022-04-10 06:48:25 +02:00 |
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