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samplesheet-check-improvement

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• c4a7d094c8 Fix EditorConfig check Sofia Stamouli 2022-10-28 14:33:44 +0200
• 5b99d9024a Add samtools stats for short-reads Sofia Stamouli 2022-10-28 14:24:33 +0200
• f87131c7b1 Save samtools stats output Sofia Stamouli 2022-10-28 14:10:24 +0200
• 1bd6dbfe58 Add samtools stats for long-reads Sofia Stamouli 2022-10-28 11:40:50 +0200
• bf89525bc2
  Merge pull request #146 from nf-core/feat-bracken Moritz E. Beber 2022-10-27 17:35:06 +0200
• 10f7f9e5de Merge branch 'adapterremoval-fix' of https://github.com/nf-core/taxprofiler into adapterremoval-fix James A. Fellows Yates 2022-10-27 12:23:52 +0000
• 08d61065e5 Add adapterlist to AR2 subworkflow James A. Fellows Yates 2022-10-27 12:23:27 +0000
• a402ee3be2 [automated] Fix linting with Prettier nf-core-bot 2022-10-27 12:20:08 +0000
• 733d3dc8c5
  Apply suggestions from code review James A. Fellows Yates 2022-10-27 14:19:28 +0200
• 76a662ecc5 Fix adapterremoval adapter conflict and add optional adapter list file James A. Fellows Yates 2022-10-27 12:17:19 +0000
• e658fab430 fix: remove def Moritz E. Beber 2022-10-27 11:50:47 +0200
• dd1a4ff158 refactor: only combine same database name Moritz E. Beber 2022-10-27 11:19:14 +0200
• 0de1ac5356 docs: add Bracken reference Moritz E. Beber 2022-10-27 10:14:57 +0200
• 63c260bfbc
  Merge pull request #148 from genomic-medicine-sweden/add_falco Sofia Stamouli 2022-10-25 12:40:26 +0200
• f4717be9ab add krakenuniq to modules.config Mahwash Jamy 2022-10-25 09:50:44 +0000
• 86ca71cfd4 include krakenuniq in profiling subworkflow Mahwash Jamy 2022-10-25 09:45:05 +0000
• 36e101a78b Install krakenuniq module Mahwash Jamy 2022-10-25 09:26:33 +0000
• de6816ec49
  Update nextflow_schema.json Sofia Stamouli 2022-10-25 11:19:16 +0200
• 7b1a53b062
  Update nextflow_schema.json Sofia Stamouli 2022-10-25 11:19:08 +0200
• 8c3e80b6ea Add helptest to nextflow_schema,add versions to longread_preprocessing Sofia Stamouli 2022-10-25 11:13:26 +0200
• 00038db634 [automated] Fix linting with Prettier nf-core-bot 2022-10-25 08:51:58 +0000
• d3d4297ca9 Apply review suggestions Sofia Stamouli 2022-10-24 16:28:07 +0200
• ca7dc308cb
  Apply suggestions from code review Moritz E. Beber 2022-10-21 16:36:35 +0200
• 60e369aa5c fix: set default run bracken to false Moritz E. Beber 2022-10-21 10:47:51 +0200
• 7bd6112133 docs: describe Bracken database usage Moritz E. Beber 2022-10-21 10:18:11 +0200
• 385507ec6f refactor: use tool name 'bracken' only Moritz E. Beber 2022-10-21 10:03:36 +0200
• 19231538da Prettier Sofia Stamouli 2022-10-20 16:59:32 +0200
• 511cb16a61 Apply review suggestions Sofia Stamouli 2022-10-20 16:55:57 +0200
• 8deb7757d8 fix: remove Bracken from standardise reports Moritz E. Beber 2022-10-19 16:21:57 +0200
• b73b479860 refactor: handle combined kraken2+bracken tool column Moritz E. Beber 2022-10-19 16:21:36 +0200
• c7c7a7f678 refactor: change Bracken prefix to be more specific Moritz E. Beber 2022-10-19 16:20:09 +0200
• 7881ba9aef Fix the amount of left-padding spaces Sofia Stamouli 2022-10-18 17:50:49 +0200
• 0481bb9449 Prettier Sofia Stamouli 2022-10-18 17:48:40 +0200
• 8eddb32b88 Add Falco as an alternative to FastQC Sofia Stamouli 2022-10-18 17:43:16 +0200
• 8768a16d63 refactor: turn warning into error Moritz E. Beber 2022-10-17 17:35:41 +0200
• 48b00b7d62 refactor: create standardized Bracken reports Moritz E. Beber 2022-10-17 17:33:24 +0200
• fd8a0df2a6 refactor: add warning when run_kraken2 is missing Moritz E. Beber 2022-10-17 17:16:21 +0200
• 563b34c9c3 refactor: rename process to kraken2 Moritz E. Beber 2022-10-14 14:48:27 +0200
• 95621ebd8a fix: include local module Moritz E. Beber 2022-10-14 14:47:08 +0200
• 4f27998852
  Update usage.md James A. Fellows Yates 2022-10-14 14:37:52 +0200
• 9dc819ceff style: reformat schema Moritz E. Beber 2022-10-14 13:16:54 +0200
• c4f6468275 chore: update parameters schema Moritz E. Beber 2022-10-14 12:55:26 +0200
• 7f8180f458 fix: emit tool versions Moritz E. Beber 2022-10-14 12:49:07 +0200
• 767663d975 chore: add Bracken to test configs Moritz E. Beber 2022-10-14 12:18:55 +0200
• ca38d002de feat: integrate Bracken into the profiling pipeline Moritz E. Beber 2022-10-14 12:18:07 +0200
• 4f728648f5 feat: add process to standardize kraken report Moritz E. Beber 2022-10-14 10:56:14 +0200
• 4352d35937 chore: install Bracken module Moritz E. Beber 2022-10-14 10:52:17 +0200
• e98cd038c7
  [skip ci] Sofia Stamouli 2022-10-12 12:56:54 +0200
• 0b16010b92
  Add tutorials section Sofia Stamouli 2022-10-12 11:39:03 +0200
• 4e771ab2c7
  Merge pull request #142 from genomic-medicine-sweden/update_readme Sofia Stamouli 2022-10-12 11:38:01 +0200
• bd56bc0ed6
  Add minimap2 and update contributors Sofia Stamouli 2022-10-12 11:10:53 +0200
• d09a8e0545
  [skip ci] Sofia Stamouli 2022-10-11 17:44:48 +0200
• 17b2ad3199 Add prettier Sofia Stamouli 2022-10-11 17:29:41 +0200
• 35b7fc26f7
  [skip ci] Sofia Stamouli 2022-10-11 17:01:08 +0200
• f22cf0c921
  Update usage.md Sofia Stamouli 2022-10-11 16:41:44 +0200
• f24344c168
  Update README.md Sofia Stamouli 2022-10-11 16:30:42 +0200
• 2423c9d87c
  Add headers Sofia Stamouli 2022-10-11 15:02:01 +0200
• dea45c66c2
  Add Krona description Sofia Stamouli 2022-10-11 14:59:48 +0200
• f25ee17fcf
  Merge pull request #141 from nf-core/minimap-patch James A. Fellows Yates 2022-10-11 12:46:26 +0200
• 56bae85755 Remove necessity of patch James Fellows Yates 2022-10-11 12:38:18 +0200
• 58dffc0c5d
  Add KrakenUniq and Filtlong in documentation Sofia Stamouli 2022-10-11 12:36:48 +0200
• ff1670169a
  Merge pull request #138 from nf-core/nf-core-template-merge-2.6 James A. Fellows Yates 2022-10-06 13:03:45 +0200
• 5f3dbd28de fix: patch inputs to correspond to previous version Moritz E. Beber 2022-10-05 13:51:15 +0200
• 180cac0395 fix: adapt to new samtools/view input Moritz E. Beber 2022-10-05 13:49:35 +0200
• f5af9fd939 fix: adjust import paths to re-organization Moritz E. Beber 2022-10-05 13:40:43 +0200
• b407fbcdce chore: force update all modules Moritz E. Beber 2022-10-05 12:24:18 +0200
• fdb8a7f740 Merge branch 'devel' into nf-core-template-merge-2.6 Moritz E. Beber 2022-10-05 12:07:22 +0200
• 51bacb00e6 Template update for nf-core/tools version 2.6 nf-core-bot 2022-10-05 03:30:53 +0000
• 3ca9058b9c
  Merge pull request #133 from rafalstepien/add-pep-support James A. Fellows Yates 2022-09-30 10:21:15 +0200
• 44146b8fe3
  Apply suggestions from code review James A. Fellows Yates 2022-09-30 08:34:53 +0200
• 8b559fba86 Pin version to get NXF to download correctly James A. Fellows Yates 2022-09-29 14:36:53 +0200
• 04d28e6520 Merge branch 'nf-core-add-pep-support' into add-pep-support Rafal Stepien 2022-09-28 14:51:38 -0400
• 00aa94a403 Merge branch 'add-pep-support' of github.com:nf-core/taxprofiler into nf-core-add-pep-support Rafal Stepien 2022-09-28 14:51:13 -0400
• bfd260e9c8 Update workflows/taxprofiler.nf Rafal Stepien 2022-09-19 09:51:25 -0400
• 87edc4569c Move to a function James Fellows Yates 2022-09-27 15:46:17 +0200
• 43a8aa4405 Remove detect_reads.py and replace remaining checks with nextflow code instead James Fellows Yates 2022-09-27 15:32:51 +0200
• 1584d6fc51 Update workflows/taxprofiler.nf Rafal Stepien 2022-09-19 09:51:25 -0400
• 0ccbf50938
  Update nextflow_schema.json Rafal Stepien 2022-09-19 09:49:37 -0400
• 5b6c18f0a2
  Update nextflow.config Rafal Stepien 2022-09-19 09:49:28 -0400
• e84b64f7e1
  Update modules/local/samplesheet_check.nf Rafal Stepien 2022-09-19 09:49:20 -0400
• 187946ec80
  Merge pull request #136 from nf-core/metaphlan3/mergemetaphlantables James A. Fellows Yates 2022-09-19 13:45:50 +0200
• 9349346864 Remove --pep parameter and leave just --input Rafal Stepien 2022-09-16 09:08:28 -0400
• 016efcb807
  Merge branch 'dev' into metaphlan3/mergemetaphlantables James A. Fellows Yates 2022-09-16 16:02:38 +0200
• a2a9f458ec
  Merge pull request #137 from nf-core/motus-merge-meta James A. Fellows Yates 2022-09-16 16:01:38 +0200
• f43c54317c
  Update subworkflows/local/standardisation_profiles.nf James A. Fellows Yates 2022-09-16 15:20:47 +0200
• 63b3cc678f Merge branch 'motus-merge-meta' of github.com:nf-core/taxprofiler into motus-merge-meta James Fellows Yates 2022-09-16 10:25:28 +0200
• c5cc21d29e Update motus merge module to remove unused channel James Fellows Yates 2022-09-16 10:25:24 +0200
• 2c83b367a7
  Apply suggestions from code review James A. Fellows Yates 2022-09-16 09:28:42 +0200
• 4e7857e2ed Standardise mOTUs table merge James Fellows Yates 2022-09-16 08:36:34 +0200
• 768f9980d8 Add pep_input_base_dir to workflow. Just need to update modules Rafal Stepien 2022-09-15 12:31:49 -0400
• cdb21d17b3
  Merge branch 'dev' into metaphlan3/mergemetaphlantables James A. Fellows Yates 2022-09-15 13:08:57 +0200
• d9795a4fdc
  Merge pull request #130 from nf-core/krakentools/combinekreports James A. Fellows Yates 2022-09-15 13:00:07 +0200
• 19a195ed14 Append profiler to resulting file James Fellows Yates 2022-09-15 12:30:39 +0200
• 21ae9d85c3 Ensure merge metaphlan3 tables happens on per database basis James Fellows Yates 2022-09-15 12:29:54 +0200
• cd83c04c98
  Merge pull request #135 from nf-core/dev-warning James A. Fellows Yates 2022-09-15 08:30:41 +0200
• 23a33a63cc
  Update README.md James A. Fellows Yates 2022-09-15 08:11:37 +0200
• 5f3eee9a4a Add working version of PEP-nf-core integration Rafal Stepien 2022-08-16 15:46:22 -0400
• 5414ae2e55
  Apply suggestions from code review James A. Fellows Yates 2022-09-14 11:20:40 +0200
• abbbf9c7ab Update to use tar module compatible for our test databases James Fellows Yates 2022-09-14 11:16:28 +0200
• 343a9e8d16
  Merge pull request #131 from nf-core/FAQs_README Sofia Stamouli 2022-09-14 09:00:17 +0200