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  • 63d9cbbdfd
         Merge pull request #80 from nf-core/activate-pipeline-specific-profiles James A. Fellows Yates 2022-05-12 11:00:49 +0200
  • aca7bc439d
         Update nextflow.config James A. Fellows Yates 2022-05-12 08:08:14 +0100
  • fd71b71929
         Merge pull request #79 from nf-core/fastp-complexity James A. Fellows Yates 2022-05-07 14:05:32 +0200
  • d67543503b
         Apply suggestions from code review James A. Fellows Yates 2022-05-07 13:15:21 +0200
  • 3fa2181f49 Fix prinseq tool selection James Fellows Yates 2022-05-07 06:15:15 +0200
  • 0f651873dd Linting James Fellows Yates 2022-05-07 06:12:24 +0200
  • 47a5ae0cff Add FASTP complexity option James Fellows Yates 2022-05-07 06:09:05 +0200
  • 87a1d80519 Add working output for Kraken2/Centrifuge/DIAMOND James Fellows Yates 2022-05-07 05:22:35 +0200
  • e7b54801ed
         Merge pull request #75 from nf-core/improve-error-message James A. Fellows Yates 2022-05-06 11:51:33 +0200
  • e52a40cc9d
         Merge pull request #77 from genomic-medicine-sweden/add_nanopore_host_reads_removal_with_minimap2 Lauri Mesilaakso 2022-05-06 12:29:17 +0300
  • 02517733aa
         Update docs/usage.md Lauri Mesilaakso 2022-05-06 10:40:59 +0200
  • b0faeedc60
         Update workflows/taxprofiler.nf Lauri Mesilaakso 2022-05-06 08:20:31 +0200
  • e3e55f57c2 Fix alignment ljmesi 2022-05-05 14:02:24 +0200
  • 6618e8cac6 Change param to a more generic name ljmesi 2022-05-05 13:20:34 +0200
  • 557d31dfd2 Add parameter for turning on longread host removal ljmesi 2022-05-05 13:19:10 +0200
  • d94534e8ac Simplify params which control host removal publish ljmesi 2022-05-05 09:07:33 +0200
  • 5b7b214156 Fix formatting with prettier ljmesi 2022-05-05 08:40:53 +0200
  • 59c7f5a5b1 Update samtools/bam2fq ljmesi 2022-05-05 08:38:41 +0200
  • f4abbe280a Fix back to nf-core modules version ljmesi 2022-05-03 12:56:49 +0200
  • c833d4fd9a Fix issues found with prettier ljmesi 2022-05-03 11:42:05 +0200
  • 58d4dec70b Update samtools view ljmesi 2022-05-03 11:09:54 +0200
  • 17039ebc6b Fix type to boolean for flags ljmesi 2022-05-03 11:07:23 +0200
  • 4b2a3789cd Update default values for host removal parameters ljmesi 2022-05-03 11:03:48 +0200
  • fa1c132635 Update nextflow_schema ljmesi 2022-05-03 11:03:25 +0200
  • afdebaf09a Remove own modification to a module ljmesi 2022-05-03 10:15:11 +0200
  • 5e6be52fab Implement hostremoval ljmesi 2022-05-03 09:34:27 +0200
  • a821f748ee Add modules ljmesi 2022-05-03 09:28:46 +0200
  • d5049a34e4 Add missing close bracket James Fellows Yates 2022-05-01 07:28:29 +0200
  • 4094706421 Only create profiler input channels when profiler activate James Fellows Yates 2022-05-01 07:24:58 +0200
  • 031cb45934 Add initial longread QC filtering - requires filtlong module update James Fellows Yates 2022-05-01 07:18:14 +0200
  • 2bae9d58ee
         Merge pull request #72 from nf-core/diamond James A. Fellows Yates 2022-04-30 20:28:28 +0200
  • 0630fce3b5 Tweak based on official DIAMOND test-data James Fellows Yates 2022-04-30 08:11:40 +0200
  • a4a9b161d8 Lintin James Fellows Yates 2022-04-29 22:02:44 +0200
  • 8126d16dee Add draft version of DIAMOND James Fellows Yates 2022-04-29 21:59:42 +0200
  • 120f86e5c7
         Merge pull request #67 from genomic-medicine-sweden/classification_kaiju2table Sofia Stamouli 2022-04-26 16:11:47 +0200
  • 194b89e66a Prettier Sofia Stamouli 2022-04-26 12:53:39 +0200
  • 7afda265c5 Enumerating taxon Sofia Stamouli 2022-04-26 11:27:18 +0200
  • f4480feb9b Prettier Sofia Stamouli 2022-04-25 17:45:26 +0200
  • d082d67bcb Add kaiju2table to taxprofiler sofstam 2022-04-25 17:36:29 +0200
  • bc84afe80d
         Merge pull request #66 from nf-core/versions-fix James A. Fellows Yates 2022-04-25 16:38:28 +0200
  • 1c694145d4
         Merge pull request #65 from genomic-medicine-sweden/classification_kreport Sofia Stamouli 2022-04-25 10:14:43 +0200
  • e3a613de00 Prettier Sofia Stamouli 2022-04-25 09:32:25 +0200
  • d8a5c793e2 Remove parameter from nextflow_schema Sofia Stamouli 2022-04-25 09:29:43 +0200
  • ba2479b95b Prettier Sofia Stamouli 2022-04-25 09:26:49 +0200
  • e7e24c2d95 Prettier and suggestions from review Sofia Stamouli 2022-04-25 09:21:29 +0200
  • 06b38f3699 Fix crash, add missing versions James Fellows Yates 2022-04-23 08:36:01 +0200
  • cda1274918 Moves ordering of modules/subworkflow versions mixing to before custom_dumpsoftwareversions mix, otherwise not used in collectFile James Fellows Yates 2022-04-23 06:47:59 +0200
  • c00ca1c2b8 Add centrifuge kreport in taxprofiler sofstam 2022-04-22 15:24:10 +0200
  • 63230c3254
         Merge pull request #63 from nf-core/maxforks James A. Fellows Yates 2022-04-21 12:57:37 +0200
  • 47a34d4c7e
         Merge pull request #59 from nf-core/hostremoval-publish-fix James A. Fellows Yates 2022-04-21 12:57:09 +0200
  • cd3c8f6a89
         Merge branch 'dev' into hostremoval-publish-fix James A. Fellows Yates 2022-04-21 11:43:06 +0200
  • d850333e11
         Linting James A. Fellows Yates 2022-04-20 13:42:26 +0200
  • d031322c16
         Update test.config James A. Fellows Yates 2022-04-20 13:41:01 +0200
  • e71e7b86a2
         Merge pull request #53 from genomic-medicine-sweden/classification_kaiju Sofia Stamouli 2022-04-20 10:57:00 +0200
  • 236141f065 Resolve conflicts with dev Sofia Stamouli 2022-04-20 10:17:10 +0200
  • 571495c812
         Merge pull request #60 from nf-core/fasta-filtering James A. Fellows Yates 2022-04-20 10:11:17 +0200
  • d16cd75652
         Merge branch 'dev' into hostremoval-publish-fix James A. Fellows Yates 2022-04-20 09:53:51 +0200
  • 53d76559af
         Merge pull request #55 from nf-core/megan-postprocessing James A. Fellows Yates 2022-04-20 09:52:55 +0200
  • fb5347a9fc
         Merge pull request #58 from nf-core/docs James A. Fellows Yates 2022-04-20 09:26:53 +0200
  • 9fd94b1389 Switch to string interpolation James Fellows Yates 2022-04-20 09:25:54 +0200
  • 60d232d62c Revert "Update subworkflows/local/profiling.nf" James Fellows Yates 2022-04-20 09:23:38 +0200
  • ac714dd30f
         Apply suggestions from code review James A. Fellows Yates 2022-04-20 09:22:10 +0200
  • b7d0557ee0
         Update subworkflows/local/profiling.nf James A. Fellows Yates 2022-04-20 09:15:45 +0200
  • 4e1b1269be Apply prettier Sofia Stamouli 2022-04-19 13:11:43 +0200
  • dc276e8bae
         Merge branch 'nf-core:dev' into classification_kaiju Sofia Stamouli 2022-04-19 13:09:15 +0200
  • 1b7ff2265d Update usage.md, reformat test.config and modules.config sofstam 2022-04-19 13:04:58 +0200
  • 87777a4289
         Update subworkflows/local/profiling.nf James A. Fellows Yates 2022-04-19 12:54:57 +0200
  • ecaff371aa
         Update input_check.nf James A. Fellows Yates 2022-04-18 07:35:19 +0200
  • 9f634805e4
         Update subworkflows/local/profiling.nf James A. Fellows Yates 2022-04-18 07:31:44 +0200
  • 9c3c8f1f4e
         Merge branch 'dev' into fasta-filtering James A. Fellows Yates 2022-04-18 07:31:14 +0200
  • 6307a9cf43 Typos James Fellows Yates 2022-04-18 07:28:09 +0200
  • 491c2d8949 Revert "Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages." James Fellows Yates 2022-04-18 07:26:15 +0200
  • 564474cafe Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages. James Fellows Yates 2022-04-18 07:21:12 +0200
  • 9880baa0b8 Get build directory working James Fellows Yates 2022-04-18 06:37:23 +0200
  • b036ed5b73 Prettier James Fellows Yates 2022-04-17 22:28:18 +0200
  • 2cfcdf2dd2 Add finer controler over for hostremoval saving James Fellows Yates 2022-04-17 22:27:04 +0200
  • 457c13e8b7 Add additional tips for host removal James Fellows Yates 2022-04-17 17:55:23 +0200
  • 818d3bd053 Complete documentation for preprocessing subworkflows James Fellows Yates 2022-04-17 17:53:22 +0200
  • d0256ec937 Prettier James Fellows Yates 2022-04-16 07:45:24 +0200
  • cc73cdd51d Add generation of taxon-table like output for MALT James Fellows Yates 2022-04-16 07:42:30 +0200
  • 6fecb3eeb7
         Merge pull request #54 from nf-core/dev James A. Fellows Yates 2022-04-16 06:17:33 +0200
  • 0e5c9e7bdd Type:boolean for kaiju in nextflow_schema.json sofstam 2022-04-14 09:14:05 +0200
  • 6736a2a980 Update README.md, nextflow_schema.json sofstam 2022-04-13 19:00:52 +0200
  • 68ce5843a4 Add kaiju in taxprofiler sofstam 2022-04-13 18:51:56 +0200
  • fc8a83245a
         Add short-read host removal via BowTie2 alignment mapping James A. Fellows Yates 2022-04-13 15:29:16 +0200
  • 5e80df0f94
         Apply suggestions from code review James A. Fellows Yates 2022-04-13 15:27:53 +0200
  • aa2d07c42a Fix merge cockup James Fellows Yates 2022-04-13 14:19:19 +0200
  • 70f94603b0
         Merge branch 'dev' into hostremoval James A. Fellows Yates 2022-04-13 13:59:51 +0200
  • 67d94a9a8d
         Merge pull request #45 from nf-core/run-merging James A. Fellows Yates 2022-04-13 12:27:37 +0200
  • dfeaa0d1fe Rename subworkflow parameters for consistency James Fellows Yates 2022-04-13 12:00:28 +0200
  • de57340526 Start work James Fellows Yates 2022-04-13 11:49:35 +0200
  • 16a3556bfc Changes after code review James Fellows Yates 2022-04-13 08:26:08 +0200
  • a15c45b00c Put map in the rigt place James Fellows Yates 2022-04-12 10:51:27 +0200
  • 8d68914192 Re-add operator name James Fellows Yates 2022-04-12 10:47:44 +0200
  • 26399718b2 Re-add pairment attachment James Fellows Yates 2022-04-12 10:46:03 +0200
  • 2ef21c6ef3 Fix input to profiling James Fellows Yates 2022-04-12 10:14:05 +0200
  • 9f221f84cc Only supply single input channel to profiling, as these are merged into single input channel at run_merging James Fellows Yates 2022-04-12 10:12:17 +0200
  • 967b1f7d6e
         Merge branch 'dev' into run-merging James A. Fellows Yates 2022-04-12 09:28:10 +0200
  • a5f4fc42d5 Fix run merging for unmerged PE data James Fellows Yates 2022-04-12 09:25:27 +0200
  • 1ac5a129a8
         Merge pull request #52 from genomic-medicine-sweden/delete_extra_directory James A. Fellows Yates 2022-04-11 20:46:50 +0200