James A. Fellows Yates
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d9003924be
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Merge pull request #201 from genomic-medicine-sweden/removo_todo
Remove TODOs from test configs
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2023-01-19 13:15:14 +01:00 |
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James Fellows Yates
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92dff9b453
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Standardise file names using only underscore
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2023-01-17 10:58:30 +01:00 |
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James Fellows Yates
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c8f6d713a3
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Add tool names to end of prefix files for easier distinguishing in general stats
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2023-01-16 14:49:44 +01:00 |
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James Fellows Yates
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d6fa45b500
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update MultiQC and include latest modules
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2023-01-16 14:39:52 +01:00 |
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James A. Fellows Yates
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25bb4304e8
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Merge pull request #187 from nf-core/revert-pep
Revert PEP validation back to python samplesheet check
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2022-12-20 15:03:18 +01:00 |
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Sofia Stamouli
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c23eb968f9
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Remove TODOs from test configs
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2022-12-16 15:20:06 +01:00 |
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James Fellows Yates
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9e6a91aff9
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Distinguish Kraken2 from Bracken
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2022-12-15 13:25:01 +01:00 |
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James Fellows Yates
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3b86a22556
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Fix falco publication names
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2022-12-15 12:57:49 +01:00 |
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James Fellows Yates
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88589fbc53
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Fix publishing of log files of rpreprocessing steps
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2022-12-15 10:35:06 +01:00 |
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James A. Fellows Yates
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578081df2e
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Merge pull request #189 from nf-core/database-check
Adds (native groovy!) database check
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2022-12-13 08:43:00 +01:00 |
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James Fellows Yates
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3df0a383da
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Update combine bracken outputs to include meta for publishing purposes
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2022-12-12 10:10:24 +01:00 |
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James Fellows Yates
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07bd989bc6
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Start work on groovy native datbase checks
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2022-12-12 10:02:22 +01:00 |
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James Fellows Yates
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4b68e95770
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Revert PEP validation back to python samplesheet check
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2022-12-12 08:49:13 +01:00 |
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James Fellows Yates
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8939ce3e20
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Start adding bracken/combinebrackenreports (need smodule update)
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2022-12-11 16:52:34 +01:00 |
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Moritz E. Beber
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4529e7e545
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refactor: change parameter exclude unmerged to include
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2022-12-04 21:36:12 +01:00 |
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James Fellows Yates
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0a0dffa37c
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Try separating MALT
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2022-12-04 12:06:33 +01:00 |
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Sofia Stamouli
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7e7299203c
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Set values to false
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2022-12-02 08:55:23 +01:00 |
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sofstam
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6d140c683a
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Merge branch 'dev' into update_motus
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2022-12-01 18:49:23 +01:00 |
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James A. Fellows Yates
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80c25008d0
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Merge pull request #177 from nf-core/sep-krakenuniq-test
Separate KrakenUniq test run
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2022-12-01 17:34:30 +01:00 |
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James A. Fellows Yates
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a34b240dfc
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Merge pull request #174 from nf-core/malt-update
Update MALT
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2022-12-01 13:58:30 +01:00 |
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James Fellows Yates
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f960c14caf
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Fix typos
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2022-12-01 13:46:57 +01:00 |
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sofstam
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38a818fd17
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Apply review suggestions
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2022-12-01 13:42:21 +01:00 |
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James A. Fellows Yates
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ef1d2da179
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-12-01 12:53:34 +01:00 |
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sofstam
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e5bb627402
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Apply review suggestions
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2022-12-01 11:12:31 +01:00 |
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James Fellows Yates
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bc98f5b80f
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Separate KrakenUniq test run
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2022-12-01 10:37:14 +01:00 |
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James A. Fellows Yates
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4f6eb6fd75
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Merge pull request #153 from mjamy/add-krakenuniq-module
Add krakenuniq module
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2022-12-01 09:03:29 +01:00 |
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sofstam
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933b820c19
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Apply review suggestions
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2022-11-29 16:57:07 +01:00 |
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James Fellows Yates
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d7fbe55849
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Add KU to the test profiles and add id to KU processes
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2022-11-29 14:19:01 +01:00 |
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Sofia Stamouli
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7e3ece53bd
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Update modules.config
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2022-11-29 13:31:00 +01:00 |
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Sofia Stamouli
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0088b07220
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Fix trailing whitespace
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2022-11-29 13:28:04 +01:00 |
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James A. Fellows Yates
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770a35d7ac
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Update conf/modules.config
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2022-11-29 12:49:20 +01:00 |
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Sofia Stamouli
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ba727a81ae
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Fix left-padding spaces
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2022-11-29 12:45:14 +01:00 |
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Sofia Stamouli
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71b52b9c94
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Apply review suggestions
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2022-11-29 11:58:23 +01:00 |
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sofstam
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49af33f68e
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Include NCBI_id, read counts and mgc arguments in motus
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2022-11-29 11:07:29 +01:00 |
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James A. Fellows Yates
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f114cc4122
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Apply suggestions from code review
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2022-11-24 16:55:19 +01:00 |
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James A. Fellows Yates
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17b1e3df1c
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Update test.config
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2022-11-24 16:53:39 +01:00 |
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James Fellows Yates
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a20b3e3c58
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Try to reduce MALT memory
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2022-11-24 15:51:12 +01:00 |
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James Fellows Yates
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9feb6c2db6
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Update MALT
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2022-11-24 14:44:04 +01:00 |
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Sofia Stamouli
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d2195e9eda
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Merge branch 'dev' into short_reads_samtools
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2022-11-04 11:47:36 +01:00 |
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Sofia Stamouli
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b5e6639f9d
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Apply review suggestions
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2022-11-03 14:12:05 +01:00 |
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James A. Fellows Yates
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bc671c547d
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Merge pull request #165 from genomic-medicine-sweden/fix_porechop_conflict
Fix porechop conflict
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2022-11-03 14:08:13 +01:00 |
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James A. Fellows Yates
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1f31f88635
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Merge pull request #158 from nf-core/adapterremoval-fix
Fix adapterremoval adapter conflict and add optional adapter list file
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2022-11-03 11:36:14 +01:00 |
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James Fellows Yates
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d487a1ff2f
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Addd FASTP adadapter list
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2022-11-02 12:39:34 +01:00 |
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Sofia Stamouli
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e4307ad8ab
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Change modules.config to include porechop_porechop
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2022-11-01 20:50:42 +01:00 |
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Mahwash Jamy
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febcbfc057
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add missing parameters to nextflow.config
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2022-10-31 16:07:53 +00:00 |
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Mahwash Jamy
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3147a80a56
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Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module
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2022-10-31 15:36:57 +00:00 |
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Sofia Stamouli
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0e0c55d3b0
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Update modules.config
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2022-10-31 12:35:51 +01:00 |
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Sofia Stamouli
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a4b5fa9f57
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Fix trailing space
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2022-10-31 12:17:49 +01:00 |
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Sofia Stamouli
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1d1047374b
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Fix EditorConfig format
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2022-10-31 12:09:25 +01:00 |
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Sofia Stamouli
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c4a7d094c8
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Fix EditorConfig check
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2022-10-28 14:33:44 +02:00 |
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Sofia Stamouli
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5b99d9024a
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Add samtools stats for short-reads
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2022-10-28 14:24:33 +02:00 |
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Sofia Stamouli
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f87131c7b1
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Save samtools stats output
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2022-10-28 14:10:24 +02:00 |
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Moritz E. Beber
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bf89525bc2
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Merge pull request #146 from nf-core/feat-bracken
add Bracken to the profiling workflow
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2022-10-27 17:35:06 +02:00 |
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James A. Fellows Yates
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76a662ecc5
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Fix adapterremoval adapter conflict and add optional adapter list file
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2022-10-27 12:17:19 +00:00 |
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Mahwash Jamy
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f4717be9ab
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add krakenuniq to modules.config
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2022-10-25 09:50:44 +00:00 |
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Moritz E. Beber
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60e369aa5c
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fix: set default run bracken to false
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2022-10-21 10:47:51 +02:00 |
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Moritz E. Beber
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c7c7a7f678
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refactor: change Bracken prefix to be more specific
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2022-10-19 16:20:09 +02:00 |
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Sofia Stamouli
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7881ba9aef
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Fix the amount of left-padding spaces
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2022-10-18 17:50:49 +02:00 |
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Sofia Stamouli
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8eddb32b88
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Add Falco as an alternative to FastQC
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2022-10-18 17:43:16 +02:00 |
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Moritz E. Beber
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767663d975
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chore: add Bracken to test configs
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2022-10-14 12:18:55 +02:00 |
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Moritz E. Beber
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ca38d002de
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feat: integrate Bracken into the profiling pipeline
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2022-10-14 12:18:07 +02:00 |
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James A. Fellows Yates
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3ca9058b9c
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Merge pull request #133 from rafalstepien/add-pep-support
Add working version of PEP-nf-core integration
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2022-09-30 10:21:15 +02:00 |
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James Fellows Yates
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43a8aa4405
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Remove detect_reads.py and replace remaining checks with nextflow code instead
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2022-09-27 15:32:51 +02:00 |
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Rafal Stepien
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9349346864
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Remove --pep parameter and leave just --input
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2022-09-16 10:14:01 -04:00 |
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James A. Fellows Yates
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016efcb807
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Merge branch 'dev' into metaphlan3/mergemetaphlantables
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2022-09-16 16:02:38 +02:00 |
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James Fellows Yates
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4e7857e2ed
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Standardise mOTUs table merge
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2022-09-16 08:36:34 +02:00 |
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James A. Fellows Yates
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cdb21d17b3
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Merge branch 'dev' into metaphlan3/mergemetaphlantables
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2022-09-15 13:08:57 +02:00 |
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James Fellows Yates
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19a195ed14
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Append profiler to resulting file
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2022-09-15 12:30:39 +02:00 |
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Rafal Stepien
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5f3eee9a4a
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Add working version of PEP-nf-core integration
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2022-09-14 14:28:48 -04:00 |
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James Fellows Yates
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05e9d92444
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Add centrigue kreports
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2022-09-13 16:47:19 +02:00 |
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James Fellows Yates
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c8dbf5be47
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Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU
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2022-09-13 15:47:28 +02:00 |
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James Fellows Yates
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a764bc4807
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Start works - need updated module though t have meta
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2022-09-09 13:57:06 +02:00 |
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James A. Fellows Yates
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cc5df924e4
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Merge branch 'dev' into module-update
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2022-09-08 13:36:21 +02:00 |
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James Fellows Yates
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fc26948950
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Fix MultiQC
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2022-09-08 12:49:38 +02:00 |
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James Fellows Yates
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832d981976
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Don't have per sample directory as unnecessary if file names are unique with the db in them
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2022-09-07 12:22:17 +02:00 |
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James Fellows Yates
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7c5f9d0c24
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Start work on more merging tools
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2022-09-06 17:34:45 +02:00 |
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James A. Fellows Yates
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dd194f3f47
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Fix mOTUs CI and old param warn
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2022-09-04 15:01:58 +00:00 |
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James A. Fellows Yates
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13e9957e14
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Fixes process selector warning
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2022-09-02 06:03:05 +00:00 |
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James A. Fellows Yates
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f7b7fd63a4
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Merge pull request #114 from nf-core/nf-core-template-merge-2.5
Important! Template update for nf-core/tools v2.5
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2022-08-31 10:28:14 +02:00 |
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James A. Fellows Yates
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28d8d3f8fb
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Merge branch 'dev' into nf-core-template-merge-2.5
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2022-08-31 09:16:34 +02:00 |
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nf-core-bot
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6dfca81761
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Template update for nf-core/tools version 2.5
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2022-08-30 13:43:03 +00:00 |
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James Fellows Yates
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afba604e8b
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Make everything within opt-out, once QC is opted-in
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2022-08-30 14:04:34 +02:00 |
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James Fellows Yates
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2cc07183a0
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Standardise QC parameter system and turn on both porechop/filtlong in tests
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2022-08-30 13:58:58 +02:00 |
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James A. Fellows Yates
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a3055bf6da
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Update conf/test_nothing.config
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2022-08-23 15:48:02 +02:00 |
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James Fellows Yates
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e6c7939305
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Add test_nothing config profile for minimal testing
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2022-08-23 14:37:01 +02:00 |
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James Fellows Yates
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a97bb69cd2
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Prettier
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2022-08-23 14:24:57 +02:00 |
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James A. Fellows Yates
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de70b0a01d
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Merge pull request #109 from nf-core/centrifuge_mqc
Trying to get Centrifuge output into MQC
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2022-07-29 13:36:25 +02:00 |
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mjamy
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5cdf5e958a
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Updated modules.config to add 'log' in diamond config
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2022-07-28 16:08:15 +02:00 |
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sofstam
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71cf32cc6a
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Add error strategy for centrifuge/kreport
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2022-07-28 08:54:32 +02:00 |
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James A. Fellows Yates
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65ae82efc4
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Define separte krakena nd centrigfue modules
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2022-07-26 18:37:33 +00:00 |
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James A. Fellows Yates
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e76b299705
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Start working getting kraken and centrifuge working in MQC
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2022-07-26 08:18:54 +00:00 |
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James Fellows Yates
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a0ee82bf43
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Add motus/merge and biom support
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2022-07-12 11:39:26 +02:00 |
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James A. Fellows Yates
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8082c7d108
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Merge pull request #97 from nf-core/malt-to-krona
Add Krona support for MALT
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2022-07-05 15:17:52 +02:00 |
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James A. Fellows Yates
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26e31c782d
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Merge branch 'dev' into motus
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2022-07-04 13:14:42 +02:00 |
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James Fellows Yates
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447b8f0905
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Get fixed Krona module and add Krona taxonomy to test profile
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2022-07-01 17:21:19 +02:00 |
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James Fellows Yates
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02c06b9f7b
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Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file
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2022-06-30 18:33:11 +02:00 |
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069370db86
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Add unclassified and verbose flags to kaiju2krona
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2022-06-28 09:00:42 -05:00 |
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18284e6e32
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Add run_krona option to allow skipping Krona chart creation
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2022-06-27 08:45:08 -05:00 |
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0e8edd5b2f
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Add output configuration for Kraken Krona chart
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2022-06-27 08:25:47 -05:00 |
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James Fellows Yates
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9462032d00
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Fix MALT save_alignemnts reads and some clean up
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2022-06-03 22:29:04 +02:00 |
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