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samplesheet-check-improvement

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• 719fc3cf5d
  Update docs/output.md Sofia Stamouli 2023-01-11 16:46:30 +0100
• 6dcf619518
  Merge pull request #209 from nf-core/module-version-bumps James A. Fellows Yates 2022-12-23 23:17:17 +0100
• e5c6db96c8 update all modules to make templaite compatible James Fellows Yates 2022-12-23 17:23:05 +0100
• ab0c62bdc1 Post-release tweaks to usage.md James Fellows Yates 2022-12-23 16:23:29 +0100
• 75a95d5ed8
  Merge pull request #143 from genomic-medicine-sweden/update_usage James A. Fellows Yates 2022-12-23 15:14:12 +0100
• acba31a8d6
  Update taxprofiler.nf James A. Fellows Yates 2022-12-23 15:08:01 +0100
• e586747680
  Add missing comma to list James A. Fellows Yates 2022-12-23 15:06:26 +0100
• 2de049399d
  Merge pull request #206 from genomic-medicine-sweden/path_params James A. Fellows Yates 2022-12-23 15:05:59 +0100
• 6ebfdcd017 Add path parameters sofstam 2022-12-23 13:40:22 +0100
• 59fd676ab3
  Merge pull request #205 from genomic-medicine-sweden/optional_untar Sofia Stamouli 2022-12-23 13:14:04 +0100
• 41c1ae9d1a
  Commit suggestion Sofia Stamouli 2022-12-23 12:20:37 +0100
• 85906ab1cb Optional untar on dbs sofstam 2022-12-23 11:25:57 +0100
• ec9c7cfedc Prettier Sofia Stamouli 2022-12-22 11:10:54 +0100
• 2f291731c1
  Merge branch 'nf-core:dev' into update_usage Sofia Stamouli 2022-12-22 11:09:50 +0100
• 1eeb3b337a
  Update usage.md Sofia Stamouli 2022-12-22 11:07:09 +0100
• 29978d83b9
  Update centrifuge section Sofia Stamouli 2022-12-22 11:03:49 +0100
• d6e0d404e3
  Update docs/usage.md Sofia Stamouli 2022-12-22 09:18:00 +0100
• ba43b0daa4
  Update docs/usage.md Sofia Stamouli 2022-12-21 09:26:38 +0100
• 35b296e5fd
  Merge pull request #202 from nf-core/nf-core-template-merge-2.7.2 Sofia Stamouli 2022-12-21 09:18:40 +0100
• 361700550e
  Merge pull request #203 from nf-core/kraken-uniq-bump James A. Fellows Yates 2022-12-20 21:51:18 +0100
• 1279437aa1
  Apply suggestions from code review James A. Fellows Yates 2022-12-20 21:48:08 +0100
• 18c15f8a78
  Update docs/output.md Sofia Stamouli 2022-12-20 20:23:38 +0100
• fb9de1e212
  Update docs/output.md Sofia Stamouli 2022-12-20 20:23:32 +0100
• 8404c28d08
  Review suggestion Sofia Stamouli 2022-12-20 20:23:26 +0100
• 1706555eff Prettier Sofia Stamouli 2022-12-20 20:10:05 +0100
• 612f532fb2 Bump KrakenUniq version James Fellows Yates 2022-12-20 20:08:12 +0100
• 24a8da2086 Fix linting Sofia Stamouli 2022-12-20 19:59:55 +0100
• 2e08c873a0
  Apply review suggestion Sofia Stamouli 2022-12-20 17:34:19 +0100
• 0cbd0a8013
  Apply review suggestion Sofia Stamouli 2022-12-20 17:33:35 +0100
• af7468522a
  Apply review suggestion Sofia Stamouli 2022-12-20 17:33:18 +0100
• 964771c5f2
  Update docs/output.md Sofia Stamouli 2022-12-20 17:33:04 +0100
• 3c33ba66ca
  Apply review suggestion Sofia Stamouli 2022-12-20 17:32:13 +0100
• af8fd18d97
  Update docs/output.md Sofia Stamouli 2022-12-20 15:44:35 +0100
• b0a6bdee5a
  Apply review suggestion Sofia Stamouli 2022-12-20 15:43:45 +0100
• c6710db7a9
  Apply review suggestion Sofia Stamouli 2022-12-20 15:42:41 +0100
• d7c4554b18
  Apply review suggestion Sofia Stamouli 2022-12-20 15:42:10 +0100
• 3eb6a29fb0
  Merge branch 'nf-core:dev' into update_output Sofia Stamouli 2022-12-20 15:30:19 +0100
• d691b89727 Merge branch 'dev' into nf-core-template-merge-2.7.2 Sofia Stamouli 2022-12-20 15:14:41 +0100
• 25bb4304e8
  Merge pull request #187 from nf-core/revert-pep James A. Fellows Yates 2022-12-20 15:03:18 +0100
• 7be3cfc450 Review suggestions Sofia Stamouli 2022-12-20 15:00:17 +0100
• 502a4a81cd
  Merge branch 'nf-core:dev' into update_usage Sofia Stamouli 2022-12-20 14:11:05 +0100
• 656956b0f9 Black formatting James Fellows Yates 2022-12-20 14:08:42 +0100
• 577da7e835 Remove .first() as the module only executes once anyway and we get a ugly warning James Fellows Yates 2022-12-20 13:59:14 +0100
• 41063bc670
  Apply suggestions from code review James A. Fellows Yates 2022-12-20 13:56:01 +0100
• 11db981a88 minor fixes James Fellows Yates 2022-12-20 13:55:15 +0100
• 7709245874
  Update subworkflows/local/input_check.nf James A. Fellows Yates 2022-12-20 13:54:05 +0100
• ab591e01ff Template update for nf-core/tools version 2.7.2 nf-core-bot 2022-12-19 12:10:58 +0000
• c23eb968f9 Remove TODOs from test configs Sofia Stamouli 2022-12-16 15:20:06 +0100
• b5c72894fd
  Merge pull request #194 from nf-core/multiqc_config Sofia Stamouli 2022-12-16 13:42:55 +0100
• 07a1cfae62
  Update assets/multiqc_config.yml Sofia Stamouli 2022-12-16 11:46:42 +0100
• 5a592f086e
  Update assets/multiqc_config.yml Sofia Stamouli 2022-12-16 11:46:35 +0100
• a2c81e33fd Prettier Sofia Stamouli 2022-12-16 08:38:58 +0100
• d6db04503e
  Configuration of multiqc report Sofia Stamouli 2022-12-15 17:04:45 +0100
• aa117e8af9
  Merge pull request #192 from nf-core/publishing-fix James A. Fellows Yates 2022-12-15 14:39:55 +0100
• 0bdc119f9c Include falco patch James Fellows Yates 2022-12-15 13:27:41 +0100
• 9e6a91aff9 Distinguish Kraken2 from Bracken James Fellows Yates 2022-12-15 13:25:01 +0100
• 3b86a22556 Fix falco publication names James Fellows Yates 2022-12-15 12:57:49 +0100
• 88589fbc53 Fix publishing of log files of rpreprocessing steps James Fellows Yates 2022-12-15 10:35:06 +0100
• 644c4ab831 Review suggestions Sofia Stamouli 2022-12-13 12:00:32 +0100
• 3282f5944b Apply prettier Sofia Stamouli 2022-12-13 11:28:17 +0100
• c9e4eba62d Prettier Sofia Stamouli 2022-12-13 11:26:06 +0100
• d99706f43d Move database section and alphabetical order sofstam 2022-12-13 11:23:07 +0100
• f80adee9e2 Review suggestions and prettier Sofia Stamouli 2022-12-13 09:50:05 +0100
• 1eb3da758b
  Apply review suggestion Sofia Stamouli 2022-12-13 09:38:09 +0100
• 97e48075c8
  Apply review suggestion Sofia Stamouli 2022-12-13 09:37:43 +0100
• 578081df2e
  Merge pull request #189 from nf-core/database-check James A. Fellows Yates 2022-12-13 08:43:00 +0100
• 971f6a6ea8
  Merge pull request #190 from nf-core/motus-update-version James A. Fellows Yates 2022-12-12 18:24:05 +0100
• 4756dc7f0d Update output.md sofstam 2022-12-12 17:14:57 +0100
• b1eb477f33 Update output.md sofstam 2022-12-12 17:06:05 +0100
• a99f89af77 Apply review suggestions Sofia Stamouli 2022-12-12 16:30:28 +0100
• e31e7d3172 Update mOTUs to 3.0.3 James Fellows Yates 2022-12-12 15:42:01 +0100
• bd5cd0a897 Prettier Sofia Stamouli 2022-12-12 13:34:53 +0100
• 896a39e68d Apply review suggestions sofstam 2022-12-12 13:19:59 +0100
• be85cb408c
  Merge pull request #188 from nf-core/bracken-mergetables James A. Fellows Yates 2022-12-12 11:26:19 +0100
• 7c66968fef More comments James Fellows Yates 2022-12-12 11:04:21 +0100
• 460f3ca157 Add database sheet validation James Fellows Yates 2022-12-12 11:03:40 +0100
• 3df0a383da Update combine bracken outputs to include meta for publishing purposes James Fellows Yates 2022-12-12 10:10:24 +0100
• 07bd989bc6 Start work on groovy native datbase checks James Fellows Yates 2022-12-12 10:02:22 +0100
• c9a6320dac Merge branch 'update_output' of https://github.com/genomic-medicine-sweden/taxprofiler into update_output sofstam 2022-12-12 09:13:02 +0100
• 4b68e95770 Revert PEP validation back to python samplesheet check James Fellows Yates 2022-12-12 08:49:13 +0100
• 8939ce3e20 Start adding bracken/combinebrackenreports (need smodule update) James Fellows Yates 2022-12-11 16:52:34 +0100
• b35d26744d Add classifiers sofstam 2022-12-09 17:11:48 +0100
• 6d0b5d0a58 Prettier Sofia Stamouli 2022-12-09 15:38:59 +0100
• 98f3ab9fd1 Apply prettier Sofia Stamouli 2022-12-09 15:35:51 +0100
• c5f4c9486a Start the documentation of output.md sofstam 2022-12-09 15:30:11 +0100
• a622dcaef0
  Delete one line Sofia Stamouli 2022-12-09 13:59:37 +0100
• 5373c58331 Merge branch 'dev' into update_usage sofstam 2022-12-09 13:05:42 +0100
• 97fbc2bceb Update usage.md sofstam 2022-12-09 12:58:51 +0100
• 13c4f44ca6
  Merge pull request #185 from nf-core/nf-core-template-merge-2.7.1 James A. Fellows Yates 2022-12-09 12:58:28 +0100
• f0846ef213 Merge branch 'update_usage' of https://github.com/genomic-medicine-sweden/taxprofiler into update_usage sofstam 2022-12-09 10:38:03 +0100
• 3af71d9c63 Merge branch 'dev' into update_usage sofstam 2022-12-09 10:35:12 +0100
• dca0b86c78 Fix versions James Fellows Yates 2022-12-09 10:28:48 +0100
• da3d2d96e6 Fix linting James Fellows Yates 2022-12-09 10:27:50 +0100
• 1ccd0a0767 Merge branch 'dev' into nf-core-template-merge-2.7.1 James Fellows Yates 2022-12-09 10:16:17 +0100
• 36f3b5723b Template update for nf-core/tools version 2.7.1 nf-core-bot 2022-12-08 13:18:23 +0000
• 1687b43596
  Merge pull request #183 from nf-core/update-bracken-params James A. Fellows Yates 2022-12-07 16:39:52 +0100
• d8751787ac Update bracken so parameters come directly from database args James Fellows Yates 2022-12-07 07:27:40 +0100
• 50da3d3efb
  Merge branch 'nf-core:dev' into update_usage Sofia Stamouli 2022-12-06 17:13:17 +0100
• 3dba6405c5 Sets correct default for --shortread_qc_mergepairs James Fellows Yates 2022-12-06 11:47:16 +0100
• 9064584356
  Merge pull request #180 from nf-core/rename-exclude-unmerged Moritz E. Beber 2022-12-05 10:53:32 +0100