millironx/taxprofiler
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  • 526ed79763 Fix filtlong logs sofstam 2022-07-19 14:01:11 +0200
  • 1ba6a08135 Seperate multiqc for filtlong sofstam 2022-07-19 13:53:29 +0200
  • 33a5402b25 Add emitting porechop logs to multiqc and fix collection of others James Fellows Yates 2022-07-19 13:50:39 +0200
  • 3f5fa8cc7a Merge branch 'dev' into update_filtlong sofstam 2022-07-19 13:50:28 +0200
  • 6f269a8245
         Merge pull request #101 from nf-core/motus/merge James A. Fellows Yates 2022-07-19 13:41:51 +0200
  • 035b4b7a17 Update the dev branch with the DIAMOND module update mjamy 2022-07-15 16:28:07 +0200
  • 5a2fd260fd Log file into multiqc channel sofstam 2022-07-15 12:50:50 +0200
  • d83c747533 Fix modules JSON James Fellows Yates 2022-07-15 12:38:20 +0200
  • c215ed5607
         Merge branch 'dev' into motus/merge James A. Fellows Yates 2022-07-15 10:52:42 +0200
  • cc3967a3fd
         Apply suggestions from code review James A. Fellows Yates 2022-07-15 10:51:41 +0200
  • 6b00360ff5 Merge branch 'dev' into update_filtlong sofstam 2022-07-15 10:05:43 +0200
  • d7ca3df160
         Merge pull request #104 from nf-core/motus-profile-update James A. Fellows Yates 2022-07-14 16:03:01 +0200
  • 449b6a5553 Fix file name output clashing wiht multiqc James Fellows Yates 2022-07-13 15:25:58 +0200
  • 31119f83c2 Send to MQC only the log file not the meta James Fellows Yates 2022-07-13 14:29:47 +0200
  • 13280e2468 Fix .empty James Fellows Yates 2022-07-13 12:44:44 +0200
  • eaa69b65d8 Update mOTUs profile module and mix log for multiqc James Fellows Yates 2022-07-13 12:38:30 +0200
  • c22946cfab Fix motu versions not being exported if not run James Fellows Yates 2022-07-13 12:36:29 +0200
  • 1fbe241d27 Update filtlong module sofstam 2022-07-12 17:43:52 +0200
  • 4a316df209 Update the dev branch with the filtlong update sofstam 2022-07-12 17:15:36 +0200
  • d8c0e9e7fe Prettier James Fellows Yates 2022-07-12 11:41:07 +0200
  • a0ee82bf43 Add motus/merge and biom support James Fellows Yates 2022-07-12 11:39:26 +0200
  • 8082c7d108
         Merge pull request #97 from nf-core/malt-to-krona James A. Fellows Yates 2022-07-05 15:17:52 +0200
  • 1eba859bf8
         Merge pull request #82 from jianhong/motus James A. Fellows Yates 2022-07-04 14:16:12 +0200
  • 26e31c782d
         Merge branch 'dev' into motus James A. Fellows Yates 2022-07-04 13:14:42 +0200
  • 447b8f0905 Get fixed Krona module and add Krona taxonomy to test profile James Fellows Yates 2022-07-01 17:21:19 +0200
  • 97e6cdf4b4 Add Krona taxonomy DB to schema build James Fellows Yates 2022-06-30 18:36:13 +0200
  • 02c06b9f7b Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file James Fellows Yates 2022-06-30 18:33:11 +0200
  • 27f174d17e Merge remote-tracking branch 'origin/dev' into malt-to-krona James Fellows Yates 2022-06-30 12:01:33 +0200
  • 0050f45345 Add taxonomy directory param James Fellows Yates 2022-06-30 11:43:52 +0200
  • 913080a5b1
         Merge pull request #96 from MillironX/feature/kaiju2krona James A. Fellows Yates 2022-06-29 09:27:25 +0200
  • 6673ccf8d8
         Update channel assignment alignment in profiling subworkflow feature/kaiju2krona Thomas A. Christensen II 2022-06-28 13:13:37 +0000
  • 069370db86
         Add unclassified and verbose flags to kaiju2krona Thomas A. Christensen II 2022-06-27 13:39:42 -0500
  • 4de43040a3
         Switch to using raw classifications for Kaiju2Krona Thomas A. Christensen II 2022-06-27 12:12:16 -0500
  • af854f5f34 Update mimetype for database csv as per https://github.com/nf-core/mag/pull/325/files James Fellows Yates 2022-06-28 12:42:41 +0200
  • e66c2b9b87
         Merge pull request #94 from MillironX/feature/centrifuge2krona James A. Fellows Yates 2022-06-27 17:13:31 +0200
  • 5e554a3a0b
         Merge pull request #91 from MillironX/feature/kreport2krona James A. Fellows Yates 2022-06-27 16:55:55 +0200
  • 821dd844d8
         Add Kaiju profile conversion to visualization workflow Thomas A. Christensen II 2022-06-27 09:23:20 -0500
  • 5b80c7cab9
         Install KAIJU_KAIJU2KRONA Thomas A. Christensen II 2022-06-27 08:58:28 -0500
  • 23fec89b06
         Add Krona chart creation for Centrifuge reports feature/centrifuge2krona Thomas A. Christensen II 2022-06-27 08:52:29 -0500
  • 18284e6e32
         Add run_krona option to allow skipping Krona chart creation feature/kreport2krona Thomas A. Christensen II 2022-06-27 08:41:42 -0500
  • 15ac8b39fa
         Add citation for Krona Thomas A. Christensen II 2022-06-14 10:54:10 -0500
  • 0e8edd5b2f
         Add output configuration for Kraken Krona chart Thomas A. Christensen II 2022-06-14 08:48:16 -0500
  • ad9bc4b7e9
         Add the visualization workflow to the main workflow Thomas A. Christensen II 2022-06-20 09:03:47 -0500
  • a40a442178
         Create VISUALIZATION_KRONA workflow to create Krona charts Thomas A. Christensen II 2022-06-27 08:22:47 -0500
  • 7af33a39b8
         Merge 7f011477a9 into 0e44098125 James A. Fellows Yates 2022-06-23 16:40:35 +0000
  • 7f011477a9 Get recominbing with databases working (still needs cleanup) James Fellows Yates 2022-06-21 09:27:07 +0200
  • bb7323ef1d Try putting MillironX's krona in subworkflow James Fellows Yates 2022-06-20 21:36:16 +0200
  • a83f53f64c
         Merge pull request #93 from nf-core/malt-rollback James A. Fellows Yates 2022-06-20 09:43:09 +0200
  • 4552b53e75 Add note about MALT version to docs James Fellows Yates 2022-06-20 08:30:23 +0200
  • 4ff2145e44 Roll back MALT version James Fellows Yates 2022-06-20 08:23:14 +0200
  • 2e7f26f380 Replace header tuple with sub-set list of only relevant columns for sample checking James A. Fellows Yates 2022-06-14 20:09:48 +0000
  • 0e44098125
         Add citation for Krona Thomas A. Christensen II 2022-06-14 10:54:10 -0500
  • be5a7fd824
         Emit visualizations channel Thomas A. Christensen II 2022-06-14 09:02:06 -0500
  • 5db450b7b5
         Add output configuration for Kraken Krona chart Thomas A. Christensen II 2022-06-14 08:48:16 -0500
  • fa87975983
         Add Krona creation and formatting to PROFILING subworkflow Thomas A. Christensen II 2022-06-14 08:48:01 -0500
  • 5da8d5b741
         Install KRONA_KTIMPORTTEXT Thomas A. Christensen II 2022-06-14 08:27:42 -0500
  • 87678c127b
         Add KRONA_CLEANUP process module Thomas A. Christensen II 2022-06-14 08:23:47 -0500
  • a84f693479
         Install KRAKENTOOLS_KREPORT2KRONA module Thomas A. Christensen II 2022-06-14 08:13:36 -0500
  • c1a7d6335f Do not require fixed column order samplesheet-check-improvement James Fellows Yates 2022-06-13 21:02:12 +0200
  • 3dcda7446b
         Merge pull request #86 from nf-core/support-aligned-reads James A. Fellows Yates 2022-06-13 11:23:34 +0200
  • e0ad49ebc9 Fix metadata manipulaton for malt James Fellows Yates 2022-06-10 19:33:37 +0200
  • 621b6a3d09
         Add comments about MALT id replacement and refactor for simplicity James A. Fellows Yates 2022-06-10 11:27:51 +0200
  • 6c6f5e0913 Merge branch 'dev' of github.com:nf-core/taxprofiler into dev James Fellows Yates 2022-06-09 08:21:51 +0200
  • ec13b8d608 Remove support for uncompressed FASTQ files James Fellows Yates 2022-06-09 08:21:48 +0200
  • 800c0dd2aa Merge branch 'support-aligned-reads' of github.com:nf-core/taxprofiler into support-aligned-reads James Fellows Yates 2022-06-09 08:16:01 +0200
  • 490a8a8a84 Remove dump James Fellows Yates 2022-06-09 08:15:58 +0200
  • dc48935651
         Apply suggestions from code review James A. Fellows Yates 2022-06-07 20:19:45 +0200
  • ebdd5683b2
         Apply suggestions from code review James A. Fellows Yates 2022-06-03 22:33:48 +0200
  • 9462032d00 Fix MALT save_alignemnts reads and some clean up James Fellows Yates 2022-06-03 22:29:04 +0200
  • 713a341e09 clean up ci.yml JIANHONG OU 2022-06-03 15:22:33 -0400
  • 9fa6ecad56 debug for database csv file JIANHONG OU 2022-06-03 14:50:03 -0400
  • 3cd3d2dad3 prettier write . JIANHONG OU 2022-06-03 14:38:59 -0400
  • 22f65eedc7 fix the download address for downloadDB for mOTUs. JIANHONG OU 2022-06-03 14:16:25 -0400
  • c8a59adbce remove the database auto-download for mOTUs. JIANHONG OU 2022-06-03 14:13:58 -0400
  • d48b3be5a7 Tweak DIAMOND save_reads message James Fellows Yates 2022-06-03 13:55:17 +0200
  • 3313b90453 Fix JSOn schema James Fellows Yates 2022-06-03 13:50:48 +0200
  • 96fecb2bfc
         Merge branch 'dev' into support-aligned-reads James A. Fellows Yates 2022-06-03 13:48:54 +0200
  • 53c4399052
         Merge branch 'dev' into motus James A. Fellows Yates 2022-06-02 21:38:35 +0200
  • 43ea8d299c
         Merge pull request #74 from nf-core/add-filtlong James A. Fellows Yates 2022-06-02 20:10:46 +0200
  • 2838c136bd Prettier James Fellows Yates 2022-06-02 12:51:39 +0200
  • c9581b1796
         Merge branch 'dev' into support-aligned-reads James A. Fellows Yates 2022-06-02 12:45:29 +0200
  • d3d28da1b1 Update after review James Fellows Yates 2022-06-02 11:53:53 +0200
  • a196e0f628
         Merge branch 'dev' into add-filtlong James A. Fellows Yates 2022-06-02 11:51:26 +0200
  • dfcaaae1fb
         Merge pull request #83 from ZandraFagernas/dev James A. Fellows Yates 2022-06-02 11:31:32 +0200
  • fa70a413cb Use finally working filtlong module James Fellows Yates 2022-05-31 21:12:09 +0200
  • 16ec5bf74a Update parameter names James Fellows Yates 2022-05-31 20:11:19 +0200
  • f0eb88cbe2 add mOTUs to modules.config JIANHONG OU 2022-05-31 08:57:00 -0400
  • 4d77b47e8d create a new test profile config for mOTUs. JIANHONG OU 2022-05-31 08:47:38 -0400
  • e916c91de3
         Delete null/pipeline_info directory JIANHONG OU 2022-05-31 07:57:15 -0400
  • 7191ad7a9b
         Merge branch 'nf-core:dev' into motus JIANHONG OU 2022-05-31 07:56:56 -0400
  • 792e2d019b Fix merge error in schema James Fellows Yates 2022-05-31 13:06:48 +0200
  • 310ac6b450 Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong James Fellows Yates 2022-05-31 13:05:52 +0200
  • 77da358e87 Separate dark and light mode logos, add to README and add to MQC report James Fellows Yates 2022-05-31 12:45:38 +0200
  • 74b48f0919
         Add files via upload ZandraFagernas 2022-05-28 13:29:24 +0200
  • f14141574e fix the end line issue for modules.json JIANHONG OU 2022-05-25 08:03:23 -0400
  • 4b3216c1cb filter fasta inputs for mOTUs; fix the typo for nopreprocessing in nextflow.config. JIANHONG OU 2022-05-24 08:42:18 -0400
  • 68d0cc00fa add motus profile. JIANHONG OU 2022-05-23 08:05:06 -0400
  • ba75685550
         Merge pull request #81 from nf-core/nf-core-template-merge-2.4 James A. Fellows Yates 2022-05-19 11:00:48 +0100
  • a9fbe47992
         Merge branch 'dev' into nf-core-template-merge-2.4 Moritz E. Beber 2022-05-19 08:42:28 +0200
  • a560492353 Template update for nf-core/tools version 2.4 TEMPLATE nf-core-bot 2022-05-16 10:22:38 +0000