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samplesheet-check-improvement

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• 9550c76c25
  Update README.md James A. Fellows Yates 2023-03-12 11:11:05 +0100
• 7f6e162e1c
  Update docs/output.md James A. Fellows Yates 2023-03-12 11:08:37 +0100
• 6266ee782d
  Update README.md James A. Fellows Yates 2023-03-12 11:08:31 +0100
• 95f9bf1fa9 Update credits section James Fellows Yates 2023-03-12 08:43:56 +0100
• e49668005f Update docs based on feedback and add missing results directories James Fellows Yates 2023-03-12 08:35:45 +0100
• efa398edab
  Merge pull request #258 from nf-core/clone-maps Moritz E. Beber 2023-03-11 21:39:49 +0100
• 5e400c8c89
  Apply suggestions from code review James A. Fellows Yates 2023-03-11 20:06:59 +0100
• bb7323e25d fix: restore setting id on FASTQ meta Moritz E. Beber 2023-03-11 11:34:47 +0100
• 7104b12e3b Update subworkflows/local/longread_preprocessing.nf Moritz E. Beber 2023-03-09 15:46:04 +0100
• fa1c779536 fix: insert id key again Moritz E. Beber 2023-03-09 15:43:58 +0100
• 246da8a7b0 chore: remove fixme comments Moritz E. Beber 2023-03-09 15:12:13 +0100
• 7c1133efb8 add more comments and slight style changes Moritz E. Beber 2023-03-07 14:57:53 +0100
• 5380bc18ec fix: channels should match 1:1 without remaining elements Moritz E. Beber 2023-03-07 13:48:38 +0100
• 07db3c93e2 style: use map addition instead of cloning Moritz E. Beber 2023-03-07 13:40:21 +0100
• d17dce5590 style: use subMap and early returns Moritz E. Beber 2023-03-07 13:25:24 +0100
• 0bcea6c993 style: use parameter for branch closure Moritz E. Beber 2023-03-07 12:40:05 +0100
• b90433f3c2 style: use parameters for filter closure Moritz E. Beber 2023-03-07 12:38:50 +0100
• aa2410a871 style: use named parameters for closure Moritz E. Beber 2023-03-07 12:35:47 +0100
• c2ad421051 refactor: simplify DB validation Moritz E. Beber 2023-03-07 12:30:02 +0100
• 53db964bcf
  Merge pull request #260 from alexhbnr/spelling_mistake_README Sofia Stamouli 2023-03-10 14:03:58 +0100
• f92a405554
  Update README.md Alex Hübner 2023-03-10 12:36:52 +0100
• c1c4180769
  Merge pull request #256 from nf-core/reduce-tests James A. Fellows Yates 2023-03-07 15:30:06 +0100
• a77517af0d
  Merge pull request #255 from nf-core/config-ordering James A. Fellows Yates 2023-03-07 15:29:32 +0100
• f3ac1d2a21 Update License to match nextflow.conifg [skip ci] James Fellows Yates 2023-03-07 14:01:09 +0100
• 6dbeb5913a
  Remove left over skips James A. Fellows Yates 2023-03-07 13:18:58 +0100
• 54e8857233
  Reduce number of tests to check just each tool option is tested James A. Fellows Yates 2023-03-07 13:06:32 +0100
• 98bc6910d5 Update authors and remove left over comment James Fellows Yates 2023-03-07 11:47:54 +0100
• 5c8e2b492c Syncronise local modules with other generic container modules James Fellows Yates 2023-03-07 11:41:57 +0100
• 91a7a03f48
  Apply suggestions from code review James A. Fellows Yates 2023-03-07 11:27:19 +0100
• e92196cd12 Remove left over comment James Fellows Yates 2023-03-07 11:10:10 +0100
• 8ca9fad3b1 move errorStrategy to config James Fellows Yates 2023-03-07 11:09:25 +0100
• b5a2983c5f Make modules entries consistent James Fellows Yates 2023-03-07 11:06:35 +0100
• d647e61a2f
  Merge pull request #253 from nf-core/futher-further-prerelease-updates Sofia Stamouli 2023-03-06 15:56:50 +0100
• 2d9dede6d4 Improve python regex James Fellows Yates 2023-03-06 12:59:08 +0100
• 6e64c2b5a9 Fix copy paste error James Fellows Yates 2023-03-06 10:50:36 +0100
• 735212c9ee Fix the non-updated KAIJU2TABLE name James Fellows Yates 2023-03-06 10:47:36 +0100
• a2a1b9cbf0 Phrasing tweak James Fellows Yates 2023-03-06 10:42:30 +0100
• 4938549d65 Clarify some documentation James Fellows Yates 2023-03-06 10:41:32 +0100
• 9ed384e0f2 Collapse FALCO and FASTQC sections, move FALCO/FASTQC sections together James Fellows Yates 2023-03-06 10:37:09 +0100
• 1f1c63bb51 Start fixing FastQC/Falco display in MultiQC James Fellows Yates 2023-03-06 09:47:26 +0100
• a5138ed6e0 Fix ugly warn when KAIJU2TABLE not run James Fellows Yates 2023-03-06 08:17:50 +0100
• f0f89eb082
  Apply suggestions from code review James A. Fellows Yates 2023-03-03 14:58:21 +0100
• c66c67524c
  Update nextflow.config James A. Fellows Yates 2023-03-03 13:33:41 +0100
• 799a44cb8c
  Merge pull request #252 from nf-core/further-prerelease-changes James A. Fellows Yates 2023-03-03 10:16:23 +0100
• 6d9cdd3c78 And the other file James Fellows Yates 2023-03-03 09:15:21 +0100
• 5feebf8d69 Fix linting issues James Fellows Yates 2023-03-03 09:12:11 +0100
• 74a5343524 Add taxpasta to tubemap James Fellows Yates 2023-03-03 09:11:10 +0100
• 6c2ce4a1c9
  Apply suggestions from code review James A. Fellows Yates 2023-03-03 08:37:31 +0100
• 0c9d6cabe8
  Merge pull request #250 from nf-core/pre-release-updates James A. Fellows Yates 2023-03-02 13:54:45 +0100
• ec89187504 Update CHANGELOG for first release James Fellows Yates 2023-03-02 13:53:32 +0100
• aedf0b34de Bump version for release James Fellows Yates 2023-03-02 13:51:28 +0100
• 5c549e5ce3 Remove TODOs and references to under development James Fellows Yates 2023-03-02 13:49:03 +0100
• a14937f668 Remove unused module and fix module structure for samplesheet_check James Fellows Yates 2023-03-02 13:34:10 +0100
• d9f687667e
  Merge pull request #249 from genomic-medicine-sweden/update_taxpasta Sofia Stamouli 2023-03-02 08:53:38 +0100
• 7ae7fb528b Prettier sofstam 2023-03-01 22:17:07 +0100
• 58f09ed659 Update taxpasta/merge module sofstam 2023-03-01 22:12:09 +0100
• b93c7082b8
  Merge pull request #248 from genomic-medicine-sweden/update_taxpasta_merge Sofia Stamouli 2023-02-27 15:19:58 +0100
• df5303270d
  Update nextflow_schema.json Sofia Stamouli 2023-02-27 14:18:30 +0100
• fff7453d0c
  Update nextflow_schema.json Sofia Stamouli 2023-02-27 14:18:22 +0100
• 9621d34c4a
  Update nextflow_schema.json Sofia Stamouli 2023-02-27 14:18:11 +0100
• 54af021965
  Update nextflow_schema.json Sofia Stamouli 2023-02-27 14:18:01 +0100
• 99fe8adb1b Add helptext sofstam 2023-02-27 13:49:02 +0100
• c94bfb0cf1 Fix prettier sofstam 2023-02-27 13:09:07 +0100
• 4dea308c22 Linting sofstam 2023-02-27 11:34:19 +0100
• 69430ef851
  Update nextflow.config Sofia Stamouli 2023-02-27 11:02:55 +0100
• e3e465df1f
  Update nextflow_schema.json Sofia Stamouli 2023-02-27 11:00:59 +0100
• d454ceed86
  Update docs/output.md Sofia Stamouli 2023-02-27 11:00:42 +0100
• 1aef73cda8
  Update docs/output.md Sofia Stamouli 2023-02-27 10:39:44 +0100
• d96e0a17a5
  Update conf/modules.config Sofia Stamouli 2023-02-27 10:39:10 +0100
• 489650feb8 Linting sofstam 2023-02-27 10:24:14 +0100
• 2f0c68a833 Last review suggestions sofstam 2023-02-27 10:15:42 +0100
• 78d7001bea Document the taxonomy parameters sofstam 2023-02-24 16:53:49 +0100
• a7ae57c94e Fix linting sofstam 2023-02-24 15:53:54 +0100
• e18e68faa5 Apply review suggestion sofstam 2023-02-24 15:50:24 +0100
• 5dc3cbc278 Rename taxonomy argument sofstam 2023-02-24 13:04:38 +0100
• 5a6fcf1f42 Update taxpasta/merge to version 0.2.0 and add taxonomy argument sofstam 2023-02-24 11:44:07 +0100
• 78c2d275e6
  Merge pull request #245 from nf-core/ku-docs [skip ci] James A. Fellows Yates 2023-02-23 14:35:54 +0100
• cd4614f387 Fix typo in schema docs [skip ci] James Fellows Yates 2023-02-23 14:00:00 +0100
• 91255b4d2d
  Merge pull request #244 from nf-core/taxpasta-ku-fix James A. Fellows Yates 2023-02-22 14:20:06 +0100
• 32c0d8d6a5
  Fix KrakenUniq Taxpasta issue James A. Fellows Yates 2023-02-22 08:24:48 +0100
• 877f6ca8b3
  Merge pull request #243 from nf-core/rma2info-label-fix James A. Fellows Yates 2023-02-20 21:46:32 +0100
• 3d1659dac7
  Merge pull request #242 from genomic-medicine-sweden/minor_fixes James A. Fellows Yates 2023-02-20 20:43:09 +0100
• 9847b8d9a7
  Fix label base.config for MEGAN_RMA2INFO James A. Fellows Yates 2023-02-20 20:35:22 +0100
• 90aa7551a9 Fix the motus_versions sofstam 2023-02-20 14:27:57 +0100
• 3fa1b0c17d Remove standardised_tables sofstam 2023-02-20 13:48:04 +0100
• 599c8d3592
  Merge pull request #241 from genomic-medicine-sweden/add_taxpasta_merge Sofia Stamouli 2023-02-20 13:15:30 +0100
• 04bc978ef6 Remove taxonomy parameter from taxpasta sofstam 2023-02-20 11:56:06 +0100
• 211b5f3a68 Apply review suggestions sofstam 2023-02-20 11:49:31 +0100
• 90a5668007 run_malt false in test and add text in output.md sofstam 2023-02-17 15:38:36 +0100
• f0aa89cb87 Rename taxpasta parameters and remove samplesheet parameter sofstam 2023-02-17 14:47:29 +0100
• 604df56fdb Add a description about the files used by taxpasta sofstam 2023-02-17 13:49:13 +0100
• 08bfa6a1a7 Apply review suggestions for docs sofstam 2023-02-17 13:43:38 +0100
• 5ebc22dd29 Add icon in nextflow_schema.json sofstam 2023-02-17 12:58:33 +0100
• 27b7171b96 Apply review suggestions sofstam 2023-02-17 09:16:58 +0100
• c9b521234b Prettier for docs sofstam 2023-02-16 16:38:00 +0100
• dad64a688d Add documentation for taxpasta module sofstam 2023-02-16 16:33:36 +0100
• 25d44c955e Merge dev into add_taxpasta_merge sofstam 2023-02-16 15:16:05 +0100
• 2456038567 Merge branch 'dev' into add_taxpasta_merge sofstam 2023-02-16 15:07:51 +0100
• bb3c49389f
  Merge pull request #240 from nf-core/move-kaiju2table James A. Fellows Yates 2023-02-16 15:03:59 +0100
• de6a4214ef Add taxpasta_merge to taxprofiler sofstam 2023-02-16 14:29:52 +0100