sofstam
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71cf32cc6a
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Add error strategy for centrifuge/kreport
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2022-07-28 08:54:32 +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 A. Fellows Yates
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8082c7d108
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Merge pull request #97 from nf-core/malt-to-krona
Add Krona support for MALT
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2022-07-05 15:17:52 +02:00 |
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James A. Fellows Yates
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26e31c782d
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Merge branch 'dev' into motus
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2022-07-04 13:14:42 +02:00 |
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James Fellows Yates
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447b8f0905
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Get fixed Krona module and add Krona taxonomy to test profile
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2022-07-01 17:21:19 +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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069370db86
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Add unclassified and verbose flags to kaiju2krona
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2022-06-28 09:00:42 -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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0e8edd5b2f
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Add output configuration for Kraken Krona chart
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2022-06-27 08:25:47 -05:00 |
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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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JIANHONG OU
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c8a59adbce
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remove the database auto-download for mOTUs.
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2022-06-03 14:13:58 -04:00 |
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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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53c4399052
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Merge branch 'dev' into motus
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2022-06-02 21:38:35 +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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d3d28da1b1
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Update after review
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2022-06-02 11:53:53 +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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JIANHONG OU
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f0eb88cbe2
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add mOTUs to modules.config
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2022-05-31 08:57:00 -04:00 |
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JIANHONG OU
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4d77b47e8d
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create a new test profile config for mOTUs.
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2022-05-31 08:47:38 -04:00 |
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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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JIANHONG OU
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68d0cc00fa
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add motus profile.
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2022-05-23 08:05:06 -04:00 |
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James A. Fellows Yates
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d67543503b
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-05-07 13:15:21 +02:00 |
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James Fellows Yates
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0f651873dd
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Linting
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2022-05-07 06:12:24 +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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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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557d31dfd2
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Add parameter for turning on longread host removal
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2022-05-05 13:19:10 +02:00 |
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ljmesi
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d94534e8ac
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Simplify params which control host removal publish
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2022-05-05 09:07:33 +02:00 |
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ljmesi
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a821f748ee
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Add modules
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2022-05-03 09:28:46 +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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0630fce3b5
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Tweak based on official DIAMOND test-data
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2022-04-30 08:11:40 +02:00 |
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James Fellows Yates
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a4a9b161d8
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Lintin
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2022-04-29 22:02:44 +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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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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