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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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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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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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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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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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 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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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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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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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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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 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 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 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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082093f3de
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Prettier
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2022-04-10 06:44:10 +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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ca011ccc5b
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Fix cat_fastq naming logic?
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2022-04-08 13:28:37 +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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Sofia Stamouli
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48d28cf8d4
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Update conf/test.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-04-08 10:00:10 +02:00 |
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Sofia Stamouli
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2dfe3b3cc1
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Update conf/test.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-04-08 10:00:04 +02:00 |
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sofstam
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26779a4420
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Remove db_name from nextflow.config
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2022-04-07 16:27:19 +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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Moritz E. Beber
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7ab3aa546b
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refactor: use flags to publish reads
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2022-04-06 10:27:11 +02:00 |
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Moritz E. Beber
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018b9a8ea6
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refactor: do not generally publish output
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2022-04-06 10:21:43 +02:00 |
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Moritz E. Beber
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8827b143a2
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fix: disable publishing correctly
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2022-04-05 20:56:19 +02:00 |
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Moritz E. Beber
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af12435fa5
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fix: use parameter for publish mode everywhere
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2022-04-05 20:56:19 +02:00 |
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Moritz E. Beber
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c40a9a0011
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refactor: avoid publishing unpacked databases
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2022-04-05 20:54:32 +02:00 |
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James Fellows Yates
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d46ddd972c
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Expand tests and fix schema after review
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2022-04-05 11:04:30 +02:00 |
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James A. Fellows Yates
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3d662d2e06
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Merge branch 'dev' into complexity-filter-bbduk
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2022-04-04 21:19:36 +02:00 |
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James Fellows Yates
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a384162810
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Add prinseq as alternative complexity filtering
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2022-04-04 21:16:51 +02:00 |
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sofstam
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d897c922b2
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Add centrifuge classificatioN
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2022-04-04 13:51:51 +02:00 |
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James A. Fellows Yates
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b2e29ea23a
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Merge branch 'dev' into hostremoval
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2022-04-03 17:24:07 +02:00 |
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James Fellows Yates
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066ceb2bca
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Remove flagstat as bowtie2 reports this itself
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2022-04-03 17:23:14 +02:00 |
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James Fellows Yates
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02d950c58c
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Fix test so complexity filter actually executes
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2022-04-02 17:18:20 +02:00 |
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James Fellows Yates
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7f1a7fb4e7
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Add complexity filtering to test profile
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2022-04-02 17:05:54 +02:00 |
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James Fellows Yates
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b055df5ea0
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Add bbduk complexity (entropy-based) filtering
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2022-04-02 17:02:05 +02:00 |
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Moritz E. Beber
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70862570e0
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fix: use same naming scheme
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2022-04-02 15:00:26 +02:00 |
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Moritz E. Beber
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817678d870
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chore: add metaphlan3 run to test profile
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2022-04-02 15:00:26 +02:00 |
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Moritz E. Beber
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b0b5936fe8
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chore: configure output for metaphlan3
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2022-04-02 15:00:26 +02:00 |
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James Fellows Yates
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dcda815bfb
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Add final adapterremoval options to match fastp functionality
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2022-04-01 09:50:08 +02:00 |
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James Fellows Yates
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76e9624e3f
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NOW commit the adapte rtrim flag
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2022-03-30 11:31:37 +02:00 |
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James Fellows Yates
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98a9688329
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Change CPUs back to template, update skiptrim fiag
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2022-03-29 15:18:06 +02:00 |
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