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  • ded6d7ab1f
         Update docs/usage.md Sofia Stamouli 2022-09-13 18:13:00 +0200
  • 0072c29a6f
         Update docs/usage.md Sofia Stamouli 2022-09-13 18:12:14 +0200
  • 05e9d92444 Add centrigue kreports James Fellows Yates 2022-09-13 16:47:19 +0200
  • c664508240
         Update usage.md Sofia Stamouli 2022-09-13 15:56:06 +0200
  • c8dbf5be47 Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU James Fellows Yates 2022-09-13 15:47:28 +0200
  • db688575f6
         Merge pull request #128 from nf-core/fastp-patch-removal James A. Fellows Yates 2022-09-09 19:07:12 +0200
  • a764bc4807 Start works - need updated module though t have meta James Fellows Yates 2022-09-09 13:57:06 +0200
  • b28052f1ec
         Remove patch from modules.json James A. Fellows Yates 2022-09-09 11:15:25 +0200
  • f087136ec9 use proper working FASTP module James Fellows Yates 2022-09-09 11:12:47 +0200
  • 3fc7f1f0f8
         Merge pull request #127 from nf-core/module-update James A. Fellows Yates 2022-09-08 16:23:44 +0200
  • 60224e9149 Patch fastp until I have an OK on the module update James Fellows Yates 2022-09-08 14:25:23 +0200
  • cc5df924e4
         Merge branch 'dev' into module-update James A. Fellows Yates 2022-09-08 13:36:21 +0200
  • 74c164bbcd
         Merge pull request #126 from nf-core/kaiju2table-move James A. Fellows Yates 2022-09-08 13:21:27 +0200
  • fc26948950 Fix MultiQC James Fellows Yates 2022-09-08 12:49:38 +0200
  • d11257b330 Module update James Fellows Yates 2022-09-08 08:08:36 +0200
  • bbd8049ca1 Remove duplicated multqic mixing James Fellows Yates 2022-09-07 13:44:08 +0200
  • 6f87c681fd
         Merge pull request #125 from nf-core/workflow-tube-map James A. Fellows Yates 2022-09-07 12:52:38 +0200
  • 832d981976 Don't have per sample directory as unnecessary if file names are unique with the db in them James Fellows Yates 2022-09-07 12:22:17 +0200
  • 3a6536b149 Add tube map properly James Fellows Yates 2022-09-07 11:22:22 +0200
  • 175be0075a Add tube map James Fellows Yates 2022-09-07 11:22:06 +0200
  • 7c5f9d0c24 Start work on more merging tools James Fellows Yates 2022-09-06 17:34:45 +0200
  • 8c6f88d1b5
         Merge pull request #118 from nf-core/motus-test-fix James A. Fellows Yates 2022-09-05 10:38:58 +0200
  • dd194f3f47 Fix mOTUs CI and old param warn James A. Fellows Yates 2022-09-04 15:01:58 +0000
  • d093de1bd0
         Merge pull request #117 from nf-core/fix-selector-warns James A. Fellows Yates 2022-09-04 16:23:53 +0200
  • 331231ea28 Standardise CI execution James A. Fellows Yates 2022-09-04 14:02:54 +0000
  • 8456f934ed
         Update subworkflows/local/visualization_krona.nf James A. Fellows Yates 2022-09-02 16:15:46 +0200
  • ef6fd002d4 Merge branch 'dev' into fix-selector-warns James Fellows Yates 2022-09-02 14:11:03 +0200
  • c9a7797682
         Merge pull request #116 from nf-core/nf-core-template-merge-2.5.1 James A. Fellows Yates 2022-09-02 13:47:39 +0200
  • c3427e44b3 Try with retries from sarek approach James Fellows Yates 2022-09-02 12:24:29 +0200
  • 3a33d81e80 Black linting I hope James Fellows Yates 2022-09-02 11:55:19 +0200
  • 7917e1d656 Synronise mOTUs CI setup James Fellows Yates 2022-09-02 11:51:18 +0200
  • 55d7919fa7 Revert "Update ci.yml" James Fellows Yates 2022-09-02 11:48:57 +0200
  • c479714a5e Revert "Update ci.yml" James Fellows Yates 2022-09-02 11:48:49 +0200
  • 8fe7f8bf4b Revert "Fix final linting problems for template merge" James Fellows Yates 2022-09-02 11:47:33 +0200
  • 61560cf065
         Update ci.yml James A. Fellows Yates 2022-09-02 10:12:27 +0200
  • 176a0a6280
         Update ci.yml James A. Fellows Yates 2022-09-02 10:06:20 +0200
  • e64b3f85a4 Fix final linting problems for template merge James A. Fellows Yates 2022-09-02 06:07:33 +0000
  • 13e9957e14 Fixes process selector warning James A. Fellows Yates 2022-09-02 06:03:05 +0000
  • 169c7437c8
         Left over from template merge James A. Fellows Yates 2022-09-01 16:28:05 +0200
  • 8fff741f85
         Merge branch 'dev' into nf-core-template-merge-2.5.1 James A. Fellows Yates 2022-09-01 16:26:45 +0200
  • 28045430d1 Template update for nf-core/tools version 2.5.1 nf-core-bot 2022-09-01 13:34:04 +0000
  • 2ca837a4a3
         Merge pull request #115 from nf-core/json-schema James A. Fellows Yates 2022-08-31 15:19:07 +0200
  • 3eb136ec3c Merge branch 'dev' into json-schema James Fellows Yates 2022-08-31 12:55:49 +0200
  • f7b7fd63a4
         Merge pull request #114 from nf-core/nf-core-template-merge-2.5 James A. Fellows Yates 2022-08-31 10:28:14 +0200
  • 394084a31b
         Merge pull request #113 from nf-core/filtlong-in-tests James A. Fellows Yates 2022-08-31 09:36:12 +0200
  • 5274ac57af
         Update .prettierignore James A. Fellows Yates 2022-08-31 09:24:24 +0200
  • 28d8d3f8fb
         Merge branch 'dev' into nf-core-template-merge-2.5 James A. Fellows Yates 2022-08-31 09:16:34 +0200
  • 0107330d92 Clarify specifying output parameters in database db_params column James Fellows Yates 2022-08-31 08:34:57 +0200
  • 806208c4b1 Final tweaks to schema, and add a couple of notes for dev guidance on where their various --save_reads parameters are injected James Fellows Yates 2022-08-31 08:30:26 +0200
  • acd0570b4a Finalise first pass of nextflow json documentation James Fellows Yates 2022-08-31 07:56:39 +0200
  • bdcae4f934 More docs and tweat to usage.md James Fellows Yates 2022-08-30 16:04:05 +0200
  • 6dfca81761 Template update for nf-core/tools version 2.5 nf-core-bot 2022-08-30 13:43:03 +0000
  • c2eaa3f6b0 Prettier James Fellows Yates 2022-08-30 14:33:40 +0200
  • d19a473c59 Merge branch 'filtlong-in-tests' into json-schema James Fellows Yates 2022-08-30 14:33:19 +0200
  • f393d1fe91
         Update nextflow.config James A. Fellows Yates 2022-08-30 14:21:20 +0200
  • 5552c264b9 Remove now unnecessary input validation James Fellows Yates 2022-08-30 14:14:01 +0200
  • 8917e29e35 Fix accidental overly zelous search-and-replace James Fellows Yates 2022-08-30 14:11:48 +0200
  • 3f8f32cba8 Make longread quality ftilering opt out James Fellows Yates 2022-08-30 14:08:05 +0200
  • afba604e8b Make everything within opt-out, once QC is opted-in James Fellows Yates 2022-08-30 14:04:34 +0200
  • 95ad380173 Turn of length filtering by default for short read (to match opt in for longread qc) James Fellows Yates 2022-08-30 14:01:52 +0200
  • 2cc07183a0 Standardise QC parameter system and turn on both porechop/filtlong in tests James Fellows Yates 2022-08-30 13:58:58 +0200
  • d4af88e3ff Make kaiju parameter clearer for documentation purpses and update documentation James Fellows Yates 2022-08-25 15:50:28 +0200
  • d6d51e0e43 Start work on reordering json schema parameters James Fellows Yates 2022-08-24 15:23:51 +0200
  • 1821496a49
         Merge pull request #90 from nf-core/samplesheet-check-improvement James A. Fellows Yates 2022-08-23 15:57:59 +0100
  • 22e03e73e3
         Merge pull request #111 from nf-core/minimal-test James A. Fellows Yates 2022-08-23 15:57:52 +0100
  • a3055bf6da
         Update conf/test_nothing.config James A. Fellows Yates 2022-08-23 15:48:02 +0200
  • 4315141c5f
         Update bin/check_samplesheet.py James A. Fellows Yates 2022-08-23 15:44:53 +0200
  • e6c7939305 Add test_nothing config profile for minimal testing James Fellows Yates 2022-08-23 14:37:01 +0200
  • a97bb69cd2 Prettier James Fellows Yates 2022-08-23 14:24:57 +0200
  • de70b0a01d
         Merge pull request #109 from nf-core/centrifuge_mqc James A. Fellows Yates 2022-07-29 13:36:25 +0200
  • 3e24f491b5
         Merge pull request #106 from nf-core/porechop-log James A. Fellows Yates 2022-07-29 10:58:12 +0200
  • f48b22d615
         Apply suggestions from code review James A. Fellows Yates 2022-07-29 09:52:49 +0200
  • 873a13e028 Merge remote-tracking branch 'origin/dev' into porechop-log James Fellows Yates 2022-07-29 09:51:34 +0200
  • 06298e867c
         Merge pull request #105 from genomic-medicine-sweden/diamond-update Mahwash Jamy 2022-07-28 17:21:59 +0200
  • 5cdf5e958a Updated modules.config to add 'log' in diamond config mjamy 2022-07-28 15:52:31 +0200
  • 49487593e2
         Merge branch 'nf-core:dev' into diamond-update Mahwash Jamy 2022-07-28 15:48:59 +0200
  • ba928af5ab
         Merge pull request #110 from genomic-medicine-sweden/update_centrifuge_kreport Sofia Stamouli 2022-07-28 10:36:30 +0200
  • 71cf32cc6a Add error strategy for centrifuge/kreport sofstam 2022-07-28 08:54:32 +0200
  • 9bc45a3f24 Update centrifuge/kreport sofstam 2022-07-27 14:44:26 +0200
  • cecbb41f88 Update centrifuge/kreport sofstam 2022-07-27 14:42:35 +0200
  • 25bcc0798d Start work on multiQC config with distinguishing Kraken/Centrifuge James Fellows Yates 2022-07-27 14:40:17 +0200
  • a3bcf8665a [automated] Fix linting with Prettier nf-core-bot 2022-07-26 18:47:40 +0000
  • 65ae82efc4 Define separte krakena nd centrigfue modules James A. Fellows Yates 2022-07-26 18:37:33 +0000
  • 9d2be68fb8 Merge branch 'dev' into centrifuge_mqc James A. Fellows Yates 2022-07-26 18:01:30 +0000
  • 1ef0975736 Merge branch 'dev' into porechop-log James A. Fellows Yates 2022-07-26 18:00:28 +0000
  • fdd9a3bc4d
         Merge pull request #107 from nf-core/fix-multiqc-mixing James A. Fellows Yates 2022-07-26 12:38:52 +0200
  • 65b0af9a8b Fix profiling channels James A. Fellows Yates 2022-07-26 08:53:43 +0000
  • 3054dea7c2 Get multiqc input working James A. Fellows Yates 2022-07-26 08:41:06 +0000
  • e76b299705 Start working getting kraken and centrifuge working in MQC James A. Fellows Yates 2022-07-26 08:18:54 +0000
  • 139cf0d6aa Fix James Fellows Yates 2022-07-26 10:12:33 +0200
  • 64f01fcfe0
         Merge branch 'dev' into porechop-log James A. Fellows Yates 2022-07-20 14:05:23 +0200
  • 1fe9c133f1
         Merge pull request #103 from genomic-medicine-sweden/update_filtlong Sofia Stamouli 2022-07-20 10:44:52 +0200
  • 255afee4c7 Re-add the collects James Fellows Yates 2022-07-19 17:10:10 +0200
  • 811ded38af
         Update subworkflows/local/profiling.nf Mahwash Jamy 2022-07-19 16:44:48 +0200
  • 237e9aa623
         Update longread_preprocessing.nf Sofia Stamouli 2022-07-19 16:44:08 +0200
  • 8d7ddb5847
         Apply suggestions from code review James A. Fellows Yates 2022-07-19 16:30:13 +0200
  • c4c82212e1 incorporate diamond log file into multiqc channel mjamy 2022-07-19 14:12:16 +0200
  • 171258d545 Fix typos sofstam 2022-07-19 14:07:13 +0200
  • 25bc01f9c4 Fix typos sofstam 2022-07-19 14:04:49 +0200
  • 8147dba0b4 Fix typos sofstam 2022-07-19 14:03:10 +0200