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  • 7dfcdd015b Re-add the 'native' combined kaiju output James Fellows Yates 2023-02-16 14:02:13 +0100
  • 4e818efe6d
         Update docs/output.md James A. Fellows Yates 2023-02-16 13:45:04 +0100
  • 79b4db9a34 Move kaiju2table to profiling James Fellows Yates 2023-02-16 13:39:05 +0100
  • 21d9135b14
         Merge pull request #238 from nf-core/process-optmisations James A. Fellows Yates 2023-02-09 15:41:30 +0100
  • ce1118930d Resource optimisation James Fellows Yates 2023-02-09 13:33:39 +0100
  • cc7d219267 Revert "optimisation for single-cpu processes" James Fellows Yates 2023-02-09 13:32:29 +0100
  • a731669b8e optimisation for single-cpu processes James Fellows Yates 2023-02-09 13:31:57 +0100
  • 45ac6fedc2
         Merge pull request #237 from nf-core/bracken-params James A. Fellows Yates 2023-02-09 10:59:27 +0100
  • 70eb84b8d5
         Apply suggestions from code review James A. Fellows Yates 2023-02-09 08:01:52 +0100
  • b3837cce5b Relax strictness so can supply empty db_params but block if only single parameter with out ; James Fellows Yates 2023-02-08 15:44:37 +0100
  • fe3d42ffd7 Make bracken db_params be a semi-colon separate list to allow kraken and bracken parameters James Fellows Yates 2023-02-08 13:34:36 +0100
  • 31d05d1994
         Merge pull request #236 from nf-core/mapped-bam-fixes James A. Fellows Yates 2023-02-07 18:42:18 +0100
  • 18886c0cbc Start trying a different method with maps in profiling James Fellows Yates 2023-02-07 15:51:25 +0100
  • 059cd17114 Fix exporting of mapped/unmapped reads for consistency across both short and long reads James Fellows Yates 2023-02-07 11:43:40 +0100
  • de5bdc36c5
         Merge pull request #230 from genomic-medicine-sweden/documentation James A. Fellows Yates 2023-02-03 16:34:09 +0100
  • 4123e06981 Apply last review suggestions sofstam 2023-02-03 15:54:29 +0100
  • 3e2b181182 Apply review suggestions sofstam 2023-02-03 15:42:45 +0100
  • ffc884b542
         Merge branch 'nf-core:dev' into documentation Sofia Stamouli 2023-02-03 15:22:51 +0100
  • 2b40d809d8
         Merge pull request #231 from nf-core/docs-t [skip ci] James A. Fellows Yates 2023-02-03 10:14:38 +0100
  • b4f88a29ce
         Update docs/usage.md [skip ci] James A. Fellows Yates 2023-02-03 09:46:01 +0100
  • 11a8624b39
         Add warning about database parameters [skip ci] James A. Fellows Yates 2023-02-03 09:42:20 +0100
  • 5363274867 Add some last documentation sofstam 2023-02-02 13:58:48 +0100
  • 2e925e5b11
         Merge pull request #229 from nf-core/full-test-profile-docs James A. Fellows Yates 2023-02-02 13:10:39 +0100
  • 7ce55a99e8 Fix linting James Fellows Yates 2023-02-02 13:08:16 +0100
  • c4e366d47d
         Add full test data and documentation of the test data James A. Fellows Yates 2023-02-02 11:59:26 +0100
  • a6b4e3c4d4
         Merge pull request #225 from nf-core/output-docs-imporvements James A. Fellows Yates 2023-01-31 13:25:07 +0100
  • 932dc12fb1 Add list of expected tools in MultiQC report [skip ci] James Fellows Yates 2023-01-31 13:09:53 +0100
  • 52907dcc26 Prettier James Fellows Yates 2023-01-31 13:07:07 +0100
  • d49344cefd
         Merge pull request #228 from nf-core/bt2-error James A. Fellows Yates 2023-01-31 13:03:53 +0100
  • 225773000f Fix channel structure when supplying own host bt2 index James Fellows Yates 2023-01-31 12:00:48 +0100
  • 43a503096e
         Merge pull request #227 from nf-core/mqc-update [skip ci] James A. Fellows Yates 2023-01-31 11:11:52 +0100
  • 01fca90496 Tweak MultiQC config [skip ci] James Fellows Yates 2023-01-31 11:08:46 +0100
  • b4d01ac226
         Formatting tweaks James A. Fellows Yates 2023-01-31 10:23:36 +0100
  • f47c294931
         Merge pull request #186 from genomic-medicine-sweden/update_output James A. Fellows Yates 2023-01-31 09:58:54 +0100
  • 366745bdbe Prettier in usage sofstam 2023-01-31 09:38:43 +0100
  • 5b738ad353 Review + prettier sofstam 2023-01-31 09:35:40 +0100
  • 1d7da61801
         Merge pull request #223 from nf-core/multiqc-tweaks James A. Fellows Yates 2023-01-30 11:25:28 +0100
  • 0edef9ea57 Review suggestions + prettier sofstam 2023-01-30 11:16:18 +0100
  • bc2876228c Apply review suggestions sofstam 2023-01-25 15:11:43 +0100
  • a77a437313 Triple patch combo! James Fellows Yates 2023-01-25 15:02:02 +0100
  • f63cec3473 Actually patch the patch James Fellows Yates 2023-01-25 14:58:19 +0100
  • d761edb615 Patch the patch James Fellows Yates 2023-01-25 14:55:57 +0100
  • 47efd193cb
         Merge pull request #219 from nf-core/allow-targz-motus [skip ci] James A. Fellows Yates 2023-01-25 13:48:43 +0100
  • 2cbb56194a
         Merge pull request #224 from nf-core/revert-metaphlan-nanopore-filter [skip ci] James A. Fellows Yates 2023-01-25 13:48:29 +0100
  • 098ec087c9
         Merge pull request #217 from nf-core/combine-kreports-fix [skip ci] James A. Fellows Yates 2023-01-25 13:48:06 +0100
  • 4f8ac72e1f Add description of each tool sofstam 2023-01-25 13:25:33 +0100
  • 5d12785ca4
         Merge branch 'nf-core:dev' into update_output Sofia Stamouli 2023-01-25 09:47:30 +0100
  • 4289e1f901
         Remove metaphlan3 nanopore filter as _sometimes_ it can work James A. Fellows Yates 2023-01-24 15:42:14 +0100
  • 7843665544 Link rather than mv James Fellows Yates 2023-01-24 15:32:49 +0100
  • c765b3f0bc
         Merge branch 'dev' into allow-targz-motus James A. Fellows Yates 2023-01-24 15:20:29 +0100
  • f940b07dfe Remove changes from other PR James Fellows Yates 2023-01-24 15:15:02 +0100
  • bdbb111344 Turn off all profilers in generla stats James Fellows Yates 2023-01-24 15:08:28 +0100
  • a993300099 Tweaks to MultiQC based on full test experiments James Fellows Yates 2023-01-24 15:06:42 +0100
  • 2431bddcbc
         Merge pull request #222 from nf-core/fix-save-minimap2 Moritz E. Beber 2023-01-24 14:57:46 +0100
  • e7d7affcd0 Pick up Kraken2 files correctly James Fellows Yates 2023-01-24 14:44:14 +0100
  • 00178d3431
         Merge pull request #221 from nf-core/metaphlan3-filter-nanopore James A. Fellows Yates 2023-01-24 14:39:02 +0100
  • 40f1e7b27a fix: correct pattern to publish minimap2 index Moritz E. Beber 2023-01-24 14:15:51 +0100
  • 14826d5205 Separate conditions, remove some left-over dumps James Fellows Yates 2023-01-24 13:20:58 +0100
  • 0358489be0 Remove metaphlan profiling for nanopore as it appears to always result in 100% unclassified James Fellows Yates 2023-01-24 13:05:52 +0100
  • 6eafcc6499
         Try Moritz's trick, assuming validate_db_rows already checks for tool name validity James A. Fellows Yates 2023-01-24 12:43:34 +0100
  • 38cbfe9a1c
         Merge pull request #220 from nf-core/sr-lr-guidance James A. Fellows Yates 2023-01-24 11:51:18 +0100
  • 9cf2d8763f
         [skip ci] Update docs/usage.md James A. Fellows Yates 2023-01-24 11:50:58 +0100
  • 4df3409f4a Merge branch 'dev' of github.com:nf-core/taxprofiler into allow-targz-motus James Fellows Yates 2023-01-24 11:50:28 +0100
  • 9205831273 Start adding filter for long read and MP3 James Fellows Yates 2023-01-24 11:50:10 +0100
  • 03ef6a69f8
         Merge pull request #215 from nf-core/remove-platform-specificity James A. Fellows Yates 2023-01-24 11:47:48 +0100
  • 085d9e519c [skip ci] add comment about recommendation to split SR/LR James Fellows Yates 2023-01-24 11:39:37 +0100
  • 2439aa69d0 Use specific samplesheet for MALT without LR reads due to GHA memory limits James Fellows Yates 2023-01-24 10:58:03 +0100
  • 1a148c5d49 Remove double If and format for readability James Fellows Yates 2023-01-24 10:48:23 +0100
  • d56e3133f9
         Allow databases of all tools to arrive as tar.gz James A. Fellows Yates 2023-01-24 10:45:01 +0100
  • 1c820f21b3 Dont fail on divide by 0 errors on centrifuge James Fellows Yates 2023-01-20 17:53:55 +0100
  • d3bad1d720
         Merge pull request #214 from nf-core/local-module-template-sync James A. Fellows Yates 2023-01-20 14:41:11 +0100
  • 606ffc0eb1 Remove platform specificity for MALT James Fellows Yates 2023-01-20 13:40:59 +0100
  • cac6f54d2d [extra] Fix warn related to recently changed parameter James Fellows Yates 2023-01-20 13:36:17 +0100
  • 2d64628552 Fix left-over warns from loca modules James Fellows Yates 2023-01-20 13:33:43 +0100
  • 7d4035d4c7
         Add new line in the description of custom file Sofia Stamouli 2023-01-19 13:44:10 +0100
  • d9003924be
         Merge pull request #201 from genomic-medicine-sweden/removo_todo James A. Fellows Yates 2023-01-19 13:15:14 +0100
  • 5162240e77
         Merge pull request #208 from nf-core/post-usage-draft-tweaks James A. Fellows Yates 2023-01-19 11:09:54 +0100
  • 36629b3dde
         Merge branch 'dev' into post-usage-draft-tweaks James A. Fellows Yates 2023-01-19 10:36:59 +0100
  • 49e4e20f84
         Merge pull request #212 from nf-core/classification-v-profiling James A. Fellows Yates 2023-01-19 10:06:15 +0100
  • 6e43695264
         Apply suggestions from code review James A. Fellows Yates 2023-01-19 08:55:23 +0100
  • 6d380fbbff
         Apply suggestions from code review James A. Fellows Yates 2023-01-19 08:49:55 +0100
  • 4dcf8c0b02 Prettier Sofia Stamouli 2023-01-17 15:50:10 +0100
  • 024b683671 Update output and usage sofstam 2023-01-17 15:38:56 +0100
  • 33d4a84237 Add explicit sentnece about classification/profiling James Fellows Yates 2023-01-17 15:23:59 +0100
  • 244fe5e30d
         Merge branch 'nf-core:dev' into update_output Sofia Stamouli 2023-01-17 14:47:56 +0100
  • 0cda0d2c51
         Merge pull request #213 from nf-core/multiqc-update James A. Fellows Yates 2023-01-17 13:37:44 +0100
  • 92dff9b453 Standardise file names using only underscore James Fellows Yates 2023-01-17 10:58:30 +0100
  • 480248bcfd Deactivate all classifer columns from general stats James Fellows Yates 2023-01-17 10:33:35 +0100
  • 11400b016c [automated] Fix linting with Prettier nf-core-bot 2023-01-16 14:11:18 +0000
  • 0947e9b8ca Fix mOTUs issues James Fellows Yates 2023-01-16 15:09:30 +0100
  • c8f6d713a3 Add tool names to end of prefix files for easier distinguishing in general stats James Fellows Yates 2023-01-16 14:49:44 +0100
  • b34a021db7
         Specify the difference between classification/profiling James A. Fellows Yates 2023-01-16 14:43:46 +0100
  • d6fa45b500 update MultiQC and include latest modules James Fellows Yates 2023-01-16 14:39:52 +0100
  • 06575b537d
         Update docs/output.md Sofia Stamouli 2023-01-16 12:59:23 +0100
  • 0e3f9f0b9a
         Update docs/output.md Sofia Stamouli 2023-01-16 12:59:13 +0100
  • 9f21181972 Add documentation for output docs sofstam 2023-01-12 15:47:29 +0100
  • 3b6be07623
         Merge branch 'nf-core:dev' into update_output Sofia Stamouli 2023-01-11 16:56:18 +0100
  • 33bce738f5
         Update docs/output.md Sofia Stamouli 2023-01-11 16:50:06 +0100
  • a49a907ad1
         Update docs/output.md Sofia Stamouli 2023-01-11 16:47:44 +0100
  • 953f9585c9
         Update docs/output.md Sofia Stamouli 2023-01-11 16:47:18 +0100