millironx/taxprofiler
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  • 989dc55ce1 Delete extra nf-core directory sofstam 2022-04-11 17:42:38 +0200
  • 78182c2a8c Add comma James Fellows Yates 2022-04-11 13:40:24 +0200
  • ff2e508a38 Merge branch 'hostremoval' of github.com:nf-core/taxprofiler into hostremoval James Fellows Yates 2022-04-11 13:38:53 +0200
  • 29073e3c93 Update CI tests James Fellows Yates 2022-04-11 13:38:42 +0200
  • 025083061e
         Merge branch 'dev' into hostremoval James A. Fellows Yates 2022-04-11 13:36:03 +0200
  • fb2f5ed73e
         Merge pull request #50 from nf-core/docs-prelim James A. Fellows Yates 2022-04-11 10:52:18 +0200
  • b8b11fd065
         Apply suggestions from code review James A. Fellows Yates 2022-04-11 10:30:29 +0200
  • b892fd0be5 Initial attempt at docs James Fellows Yates 2022-04-10 22:17:44 +0200
  • dd22e042be
         Merge pull request #47 from nf-core/profiling-subworkflow James A. Fellows Yates 2022-04-10 16:54:35 +0200
  • 030099c559 A bit of clean up James Fellows Yates 2022-04-10 07:26:20 +0200
  • 80c08af11b Mix in profiling versions into mainline versons channel James Fellows Yates 2022-04-10 06:48:25 +0200
  • 082093f3de Prettier James Fellows Yates 2022-04-10 06:44:10 +0200
  • ecf0eea4f9 Move profiling to subworkflow and standardise outputs James Fellows Yates 2022-04-10 06:43:30 +0200
  • afb66e445f Append pairment to ID at profiling to prevent multiqc-level filename crash James Fellows Yates 2022-04-08 21:36:59 +0200
  • 8839fe22b8 Fix output tuple for reads James Fellows Yates 2022-04-08 20:02:22 +0200
  • 35cb6e042a Flatten the right thing James Fellows Yates 2022-04-08 13:46:12 +0200
  • 6c14f2b230 Remove the flattening? James Fellows Yates 2022-04-08 13:44:52 +0200
  • a634814d84 Formatting and fix fastp output James Fellows Yates 2022-04-08 13:34:00 +0200
  • ca011ccc5b Fix cat_fastq naming logic? James Fellows Yates 2022-04-08 13:28:37 +0200
  • d130a72d74 Get this working James Fellows Yates 2022-04-08 13:09:23 +0200
  • 4d726a87e9 Fix metadata removal James Fellows Yates 2022-04-08 12:01:07 +0200
  • 74c496f6af Fix CAT_FASTQ output James Fellows Yates 2022-04-08 11:58:16 +0200
  • 7b08c49cd6 Re-add run merging and gonna let GHA see if it works >.> James Fellows Yates 2022-04-08 11:54:54 +0200
  • 5f24f94391
         Merge pull request #31 from genomic-medicine-sweden/classification_centrifuge Sofia Stamouli 2022-04-08 11:26:57 +0200
  • 63bc597daf Prettier Sofia Stamouli 2022-04-08 11:01:45 +0200
  • fd5ebea9a6 Remove old centrifuge module Sofia Stamouli 2022-04-08 10:57:58 +0200
  • 48d28cf8d4
         Update conf/test.config Sofia Stamouli 2022-04-08 10:00:10 +0200
  • 2dfe3b3cc1
         Update conf/test.config Sofia Stamouli 2022-04-08 10:00:04 +0200
  • 3d45ac57ae Prettier Sofia Stamouli 2022-04-07 16:42:22 +0200
  • 26779a4420 Remove db_name from nextflow.config sofstam 2022-04-07 16:27:19 +0200
  • 606e5da7d5 Check if PR works with centrifuge/centrifuge module sofstam 2022-04-07 16:13:17 +0200
  • b554aa3e4d
         Merge branch 'dev' into hostremoval James A. Fellows Yates 2022-04-07 14:00:10 +0200
  • 4c4475c316
         Merge pull request #43 from nf-core/refactor-config James A. Fellows Yates 2022-04-06 11:03:45 +0200
  • 7ab3aa546b refactor: use flags to publish reads Moritz E. Beber 2022-04-06 10:27:11 +0200
  • 018b9a8ea6 refactor: do not generally publish output Moritz E. Beber 2022-04-06 10:21:43 +0200
  • 8827b143a2 fix: disable publishing correctly Moritz E. Beber 2022-04-05 12:30:06 +0200
  • af12435fa5 fix: use parameter for publish mode everywhere Moritz E. Beber 2022-04-05 12:16:26 +0200
  • c40a9a0011 refactor: avoid publishing unpacked databases Moritz E. Beber 2022-04-05 12:13:45 +0200
  • e72be724a6
         Merge pull request #36 from nf-core/complexity-filter-bbduk James A. Fellows Yates 2022-04-05 16:45:40 +0200
  • 82aa89ad63 re add missing switch meta of merged reads to true James Fellows Yates 2022-04-05 13:55:11 +0200
  • 98f082d7b6 Fix mistake in previous upstream merge with AR2 output channel for settings file James Fellows Yates 2022-04-05 13:17:54 +0200
  • 4dbd0ddc73 Merge branch 'complexity-filter-bbduk' of github.com:nf-core/taxprofiler into complexity-filter-bbduk James Fellows Yates 2022-04-05 13:14:13 +0200
  • 5b9355725d Whoops James Fellows Yates 2022-04-05 13:14:06 +0200
  • 23fb319779
         Merge branch 'dev' into complexity-filter-bbduk James A. Fellows Yates 2022-04-05 13:11:15 +0200
  • 245a4d1f5d Fix MQC staging and remove debugging dump James Fellows Yates 2022-04-05 13:08:44 +0200
  • b37a9c5576
         Merge pull request #42 from nf-core/refactor-adapterremoval Moritz E. Beber 2022-04-05 12:04:36 +0200
  • 39e5e802c7 refactor: make code more explicit, add comment Moritz E. Beber 2022-04-05 11:29:39 +0200
  • 59b2088aa1 style: apply prettier Moritz E. Beber 2022-04-05 11:16:43 +0200
  • d46ddd972c Expand tests and fix schema after review James Fellows Yates 2022-04-05 11:04:30 +0200
  • 0e9b2989e3 refactor: remove superfluous ENSURE_FASTQ_EXTENSION Moritz E. Beber 2022-04-05 10:53:04 +0200
  • c54c32c494 chore: update adapterremoval Moritz E. Beber 2022-04-05 10:18:34 +0200
  • bb6dd738bd Merge branch 'complexity-filter-bbduk' of github.com:nf-core/taxprofiler into complexity-filter-bbduk James Fellows Yates 2022-04-04 21:21:34 +0200
  • 613f6a5565 Prettier James Fellows Yates 2022-04-04 21:21:29 +0200
  • 3d662d2e06
         Merge branch 'dev' into complexity-filter-bbduk James A. Fellows Yates 2022-04-04 21:19:36 +0200
  • a384162810 Add prinseq as alternative complexity filtering James Fellows Yates 2022-04-04 21:16:51 +0200
  • 3a56206513 Centrifuge classification sofstam 2022-04-04 16:55:48 +0200
  • d897c922b2 Add centrifuge classificatioN sofstam 2022-04-04 13:51:51 +0200
  • a76576c16b Prettier James Fellows Yates 2022-04-03 17:24:50 +0200
  • b2e29ea23a
         Merge branch 'dev' into hostremoval James A. Fellows Yates 2022-04-03 17:24:07 +0200
  • 066ceb2bca Remove flagstat as bowtie2 reports this itself James Fellows Yates 2022-04-03 17:23:14 +0200
  • fe628b3578
         Merge pull request #29 from nf-core/add-metaphlan Moritz E. Beber 2022-04-03 09:08:01 +0200
  • 482112bb42 Start work on host removal James Fellows Yates 2022-04-03 07:58:40 +0200
  • d3572e1878 Final MQC fix for AR2 (remove too-early collect) James Fellows Yates 2022-04-03 07:28:01 +0200
  • f5baf910be
         Apply suggestions from code review Moritz E. Beber 2022-04-03 00:21:09 +0200
  • be93eae640 fix: insert .fastq file extension Moritz E. Beber 2022-04-02 21:50:13 +0200
  • 02d950c58c Fix test so complexity filter actually executes James Fellows Yates 2022-04-02 17:18:20 +0200
  • 469e4f3682 Remove remaining debugging .dumps( James Fellows Yates 2022-04-02 17:07:30 +0200
  • 7f1a7fb4e7 Add complexity filtering to test profile James Fellows Yates 2022-04-02 17:05:54 +0200
  • 4eab257d68 style: prettify comment Moritz E. Beber 2022-04-02 17:05:46 +0200
  • b055df5ea0 Add bbduk complexity (entropy-based) filtering James Fellows Yates 2022-04-02 17:02:05 +0200
  • 41526e8a64 try to fix locale Moritz E. Beber 2022-04-02 15:44:39 +0200
  • 4e22bc9610 fix: force UTF-8 in different locale? Moritz E. Beber 2022-04-02 15:20:36 +0200
  • 562fa42696 fix: remove duplicate porechop entry Moritz E. Beber 2022-04-02 15:00:55 +0200
  • 70862570e0 fix: use same naming scheme Moritz E. Beber 2022-04-02 14:58:07 +0200
  • 817678d870 chore: add metaphlan3 run to test profile Moritz E. Beber 2022-04-02 14:45:07 +0200
  • 996b3f4912 fix: correct the input shape to metaphlan3 Moritz E. Beber 2022-04-02 14:44:48 +0200
  • b0b5936fe8 chore: configure output for metaphlan3 Moritz E. Beber 2022-04-02 14:44:27 +0200
  • 95ed86516b chore: add citation Moritz E. Beber 2022-04-02 13:59:10 +0200
  • e579f9f5f3 style: apply prettier Moritz E. Beber 2022-04-02 00:28:54 +0200
  • fb9afa013a fix: add metaphlan parameter to schema Moritz E. Beber 2022-04-01 16:33:22 +0200
  • a425a322f2 refactor: make metaphlan3 run in workflow Moritz E. Beber 2022-03-18 20:50:18 +0100
  • 69db920610 feat: include metaphlan3 in workflow Moritz E. Beber 2022-03-18 16:01:33 +0100
  • 4d2960c06f chore: add metaphlan3 module Moritz E. Beber 2022-03-18 15:38:19 +0100
  • 1dfbcacf68
         Merge pull request #34 from nf-core/adapterremoval James A. Fellows Yates 2022-04-02 10:33:45 +0200
  • 93aaa9eeac Clean up AdapterRemoval and remove all debugging dumps James Fellows Yates 2022-04-01 21:36:22 +0200
  • 03e832954f
         Update subworkflows/local/shortread_adapterremoval.nf James A. Fellows Yates 2022-04-01 20:55:33 +0200
  • 14f2b7bd84
         Apply suggestions from code review James A. Fellows Yates 2022-04-01 15:34:05 +0200
  • 0d0b377dfb Add additional test James Fellows Yates 2022-04-01 11:19:00 +0200
  • df4f13319f More linting James Fellows Yates 2022-04-01 11:13:57 +0200
  • b04cfec2c2 Prettier linting James Fellows Yates 2022-04-01 11:13:36 +0200
  • dcda815bfb Add final adapterremoval options to match fastp functionality James Fellows Yates 2022-04-01 09:50:08 +0200
  • c4c93bd59d Start working on adding adapterremoval James Fellows Yates 2022-03-31 15:31:45 +0200
  • 323883bd3e
         Merge pull request #33 from nf-core/improve-shortread-input James A. Fellows Yates 2022-03-30 11:48:32 +0200
  • 76e9624e3f NOW commit the adapte rtrim flag James Fellows Yates 2022-03-30 11:31:37 +0200
  • 98a9688329 Change CPUs back to template, update skiptrim fiag James Fellows Yates 2022-03-29 15:18:06 +0200
  • c552819c72 Apply prettier again Sofia Stamouli 2022-03-28 22:15:31 +0200
  • d25f97c506 Prettier format sofstam 2022-03-28 22:08:05 +0200
  • 04fb6f4127 Use new resources for test data James Fellows Yates 2022-03-28 20:38:16 +0200
  • 94e5cfef4a Filter long reads for MALT, bump cpus for FastQC for minigut to pass James Fellows Yates 2022-03-28 18:20:10 +0200
  • eada201eb2 Prettier James Fellows Yates 2022-03-28 16:47:37 +0200