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• 24e5bc5410 refactor: use shorter and more explicit syntax Moritz E. Beber 2022-12-04 21:54:10 +0100
• b2088bcbb3 docs: improve description of shortread_qc_includeunmerged Moritz E. Beber 2022-12-04 21:53:38 +0100
• 4529e7e545 refactor: change parameter exclude unmerged to include Moritz E. Beber 2022-12-01 17:25:25 +0100
• 7992edd181
  Merge pull request #181 from nf-core/sep-krakenuniq-test James A. Fellows Yates 2022-12-04 13:57:11 +0100
• 0a0dffa37c Try separating MALT James Fellows Yates 2022-12-04 12:06:33 +0100
• 0dccfddc24 Switch order back James Fellows Yates 2022-12-03 21:38:25 +0100
• cf8ad96771
  Update subworkflows/local/profiling.nf James A. Fellows Yates 2022-12-02 15:09:08 +0100
• ab42f6b662 wteak message James Fellows Yates 2022-12-02 12:49:00 +0100
• a3cd188b1f Merge branch 'sep-krakenuniq-test' of github.com:nf-core/taxprofiler into sep-krakenuniq-test James Fellows Yates 2022-12-02 12:48:18 +0100
• de74e4f727 Fix centrifuge warning, filter out long reads from Brakcen, add some caveat docs to usage.md James Fellows Yates 2022-12-02 12:47:14 +0100
• c56c6ea694
  Merge pull request #176 from nf-core/update_motus Sofia Stamouli 2022-12-02 12:18:58 +0100
• 7e7299203c
  Set values to false Sofia Stamouli 2022-12-02 08:55:23 +0100
• 6d140c683a Merge branch 'dev' into update_motus sofstam 2022-12-01 18:49:23 +0100
• 80c25008d0
  Merge pull request #177 from nf-core/sep-krakenuniq-test James A. Fellows Yates 2022-12-01 17:34:30 +0100
• 410196c37b [automated] Fix linting with Prettier nf-core-bot 2022-12-01 14:33:34 +0000
• 4800a5f03e Update schema sofstam 2022-12-01 14:23:40 +0100
• a34b240dfc
  Merge pull request #174 from nf-core/malt-update James A. Fellows Yates 2022-12-01 13:58:30 +0100
• f960c14caf Fix typos James Fellows Yates 2022-12-01 13:46:57 +0100
• 38a818fd17 Apply review suggestions sofstam 2022-12-01 13:42:21 +0100
• ef1d2da179
  Apply suggestions from code review James A. Fellows Yates 2022-12-01 12:53:34 +0100
• 1965ade961 Update schema sofstam 2022-12-01 11:32:51 +0100
• e5bb627402 Apply review suggestions sofstam 2022-12-01 11:12:31 +0100
• bc98f5b80f Separate KrakenUniq test run James Fellows Yates 2022-12-01 10:37:14 +0100
• 8067012c01 [automated] Fix linting with Prettier nf-core-bot 2022-12-01 09:15:35 +0000
• 4f6eb6fd75
  Merge pull request #153 from mjamy/add-krakenuniq-module James A. Fellows Yates 2022-12-01 09:03:29 +0100
• 933b820c19 Apply review suggestions sofstam 2022-11-29 16:57:07 +0100
• e85c75dcba
  Merge branch 'dev' into update_motus Sofia Stamouli 2022-11-29 15:12:31 +0100
• 12dd836e9c Fix conflict sofstam 2022-11-29 15:00:27 +0100
• f389029848 Fix merge conflic sofstam 2022-11-29 14:38:39 +0100
• d7fbe55849 Add KU to the test profiles and add id to KU processes James Fellows Yates 2022-11-29 14:19:01 +0100
• 7e3ece53bd
  Update modules.config Sofia Stamouli 2022-11-29 13:31:00 +0100
• 0088b07220
  Fix trailing whitespace Sofia Stamouli 2022-11-29 13:28:04 +0100
• 770a35d7ac
  Update conf/modules.config James A. Fellows Yates 2022-11-29 12:49:20 +0100
• ba727a81ae Fix left-padding spaces Sofia Stamouli 2022-11-29 12:45:14 +0100
• 71b52b9c94 Apply review suggestions Sofia Stamouli 2022-11-29 11:58:23 +0100
• 3d949a803f
  Merge pull request #175 from nf-core/schema-clean James A. Fellows Yates 2022-11-29 11:49:27 +0100
• fb6be69d7e Prettier should work now Sofia Stamouli 2022-11-29 11:37:20 +0100
• 644a29c699 Prettier sofstam 2022-11-29 11:34:57 +0100
• 5254b8d679 Prettier sofstam 2022-11-29 11:25:52 +0100
• 0235ef42ca Update nextflow_schema.json sofstam 2022-11-29 11:15:40 +0100
• 49af33f68e Include NCBI_id, read counts and mgc arguments in motus sofstam 2022-11-29 11:07:29 +0100
• af8ce2cbfd chore: update krakenuniq Moritz E. Beber 2022-11-29 10:27:35 +0100
• d6c0ebb4c6 Prettier James Fellows Yates 2022-11-29 10:14:33 +0100
• ddcf38de22 refactor: make mappings explicit Moritz E. Beber 2022-11-29 10:14:20 +0100
• f13185d98b Fix schema location ofr fastqc/falco option James Fellows Yates 2022-11-29 10:13:46 +0100
• f114cc4122
  Apply suggestions from code review James A. Fellows Yates 2022-11-24 16:55:19 +0100
• 17b1e3df1c
  Update test.config James A. Fellows Yates 2022-11-24 16:53:39 +0100
• a20b3e3c58 Try to reduce MALT memory James Fellows Yates 2022-11-24 15:51:12 +0100
• 131b39aa8b Fix linting James Fellows Yates 2022-11-24 15:49:06 +0100
• 9feb6c2db6 Update MALT James Fellows Yates 2022-11-24 14:44:04 +0100
• f8b769a8f0
  Merge pull request #172 from genomic-medicine-sweden/update_samtools_stats Sofia Stamouli 2022-11-23 10:21:47 +0100
• 481f90589c Apply review suggestions sofstam 2022-11-23 09:08:22 +0100
• b6f5930b49
  Merge pull request #171 from nf-core/chore-fail-slow Moritz E. Beber 2022-11-22 19:22:14 +0100
• 30af26a8b3 Include the mapped reads in samtools stats sofstam 2022-11-22 16:50:50 +0100
• a383c9ae40 Remove the join James Fellows Yates 2022-11-22 13:39:21 +0100
• 06659af777 Remove flatten James Fellows Yates 2022-11-22 13:36:40 +0100
• cacd7d3128 Not just in stub James Fellows Yates 2022-11-22 13:33:13 +0100
• e8de006ed6 With a join James Fellows Yates 2022-11-22 13:27:49 +0100
• ebfc84e235 Does the grouping work if we have meta? James Fellows Yates 2022-11-22 13:26:54 +0100
• 21759807f7 Does flatten work? James Fellows Yates 2022-11-22 12:48:54 +0100
• 3102e40052 dump teh db James Fellows Yates 2022-11-22 12:46:26 +0100
• 557f2a4d96 Extra dump James Fellows Yates 2022-11-22 12:26:46 +0100
• 5caebcc6ab Append to correct db James Fellows Yates 2022-11-22 12:21:59 +0100
• 52fc00802b Correct meta name for db meta James Fellows Yates 2022-11-22 12:19:56 +0100
• b8937748d3 Fix meta.id isssue James Fellows Yates 2022-11-22 12:18:52 +0100
• db334c5185 Fix missing info James Fellows Yates 2022-11-22 12:17:08 +0100
• 0f298dca43 group krakenuniq reads by pairs or single end James Fellows Yates 2022-11-22 12:13:08 +0100
• 6b538d658a chore: let all tests run to completion Moritz E. Beber 2022-11-22 10:13:10 +0100
• 10c72f1265
  Merge pull request #169 from nf-core/diagram-update James A. Fellows Yates 2022-11-06 10:15:56 +0100
• f414f5dc9c Add falco to tube map James Fellows Yates 2022-11-04 18:20:44 +0100
• 4275640d9b update tubemap to include samtools stats James Fellows Yates 2022-11-04 15:24:15 +0100
• 67e264b7a9
  Merge pull request #162 from genomic-medicine-sweden/short_reads_samtools James A. Fellows Yates 2022-11-04 14:39:29 +0100
• 696edfb866 Apply prettier Sofia Stamouli 2022-11-04 12:05:23 +0100
• d2195e9eda
  Merge branch 'dev' into short_reads_samtools Sofia Stamouli 2022-11-04 11:47:36 +0100
• 79dd3930bb
  Add samtools to README Sofia Stamouli 2022-11-03 16:52:01 +0100
• 461482d22a Try again wit hthe corret param James Fellows Yates 2022-11-03 15:02:22 +0100
• 93f38b14a8 Save report James Fellows Yates 2022-11-03 15:01:00 +0100
• c5e5696f84 Fix parameter name James Fellows Yates 2022-11-03 14:58:03 +0100
• c03a21c770 Merge branch 'add-krakenuniq-module' of github.com:mjamy/taxprofiler into add-krakenuniq-module James Fellows Yates 2022-11-03 14:56:43 +0100
• 21a76c2449 Fix cardinality issue James Fellows Yates 2022-11-03 14:56:26 +0100
• 0c445759e4 [automated] Fix linting with Prettier nf-core-bot 2022-11-03 13:42:39 +0000
• b5e6639f9d
  Apply review suggestions Sofia Stamouli 2022-11-03 14:12:05 +0100
• bc671c547d
  Merge pull request #165 from genomic-medicine-sweden/fix_porechop_conflict James A. Fellows Yates 2022-11-03 14:08:13 +0100
• 6459d8920f Linting! James Fellows Yates 2022-11-03 14:05:43 +0100
• 1f31f88635
  Merge pull request #158 from nf-core/adapterremoval-fix James A. Fellows Yates 2022-11-03 11:36:14 +0100
• 62f45c8be7
  Update nextflow.config James A. Fellows Yates 2022-11-03 10:03:27 +0100
• 24dc2a2cec
  Apply suggestions from code review James A. Fellows Yates 2022-11-03 10:03:07 +0100
• d487a1ff2f Addd FASTP adadapter list James Fellows Yates 2022-11-02 12:39:34 +0100
• e4307ad8ab Change modules.config to include porechop_porechop Sofia Stamouli 2022-11-01 20:50:42 +0100
• 3faea8aac5 Fix porechop conflict Sofia Stamouli 2022-11-01 17:34:37 +0100
• aecf308840 Update documentation for krakenuniq Mahwash Jamy 2022-10-31 16:41:35 +0000
• 851016e497 Update nextflow_scheme.json Mahwash Jamy 2022-10-31 16:17:40 +0000
• febcbfc057 add missing parameters to nextflow.config Mahwash Jamy 2022-10-31 16:07:53 +0000
• 3147a80a56 Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module Mahwash Jamy 2022-10-31 15:36:57 +0000
• 0e0c55d3b0
  Update modules.config Sofia Stamouli 2022-10-31 12:35:51 +0100
• a4b5fa9f57
  Fix trailing space Sofia Stamouli 2022-10-31 12:17:49 +0100
• 1d1047374b
  Fix EditorConfig format Sofia Stamouli 2022-10-31 12:09:25 +0100
• 074d3ec204
  Merge pull request #161 from genomic-medicine-sweden/samtools_stats Sofia Stamouli 2022-10-31 10:59:37 +0100
• ce611d6efd Add bowtie2 mapped reads Sofia Stamouli 2022-10-31 10:04:51 +0100
• f1778acf35
  Apply review suggestion Sofia Stamouli 2022-10-31 09:31:13 +0100