James A. Fellows Yates
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142ff2f099
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Apply suggestions from code review
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2023-03-17 10:26:38 +01:00 |
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James Fellows Yates
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577d270423
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Deactivate saving of reads and other large files for full tests
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2023-03-17 10:14:40 +01:00 |
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James Fellows Yates
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8ca9fad3b1
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move errorStrategy to config
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2023-03-07 11:09:25 +01:00 |
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James Fellows Yates
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b5a2983c5f
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Make modules entries consistent
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2023-03-07 11:06:35 +01:00 |
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James Fellows Yates
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a5138ed6e0
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Fix ugly warn when KAIJU2TABLE not run
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2023-03-06 08:17:50 +01:00 |
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James A. Fellows Yates
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6c2ce4a1c9
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Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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2023-03-03 08:37:31 +01:00 |
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James Fellows Yates
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5c549e5ce3
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Remove TODOs and references to under development
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2023-03-02 13:49:03 +01:00 |
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Sofia Stamouli
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d96e0a17a5
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Update conf/modules.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2023-02-27 10:39:10 +01:00 |
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sofstam
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2f0c68a833
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Last review suggestions
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2023-02-27 10:15:42 +01:00 |
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sofstam
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a7ae57c94e
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Fix linting
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2023-02-24 15:53:54 +01:00 |
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sofstam
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e18e68faa5
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Apply review suggestion
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2023-02-24 15:50:24 +01:00 |
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sofstam
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5dc3cbc278
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Rename taxonomy argument
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2023-02-24 13:04:38 +01:00 |
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sofstam
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5a6fcf1f42
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Update taxpasta/merge to version 0.2.0 and add taxonomy argument
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2023-02-24 11:44:07 +01:00 |
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James A. Fellows Yates
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9847b8d9a7
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Fix label base.config for MEGAN_RMA2INFO
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2023-02-20 20:35:22 +01:00 |
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sofstam
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04bc978ef6
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Remove taxonomy parameter from taxpasta
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2023-02-20 11:56:06 +01:00 |
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sofstam
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90a5668007
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run_malt false in test and add text in output.md
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2023-02-17 15:38:36 +01:00 |
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sofstam
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f0aa89cb87
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Rename taxpasta parameters and remove samplesheet parameter
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2023-02-17 14:47:29 +01:00 |
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sofstam
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27b7171b96
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Apply review suggestions
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2023-02-17 09:16:58 +01:00 |
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sofstam
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2456038567
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Merge branch 'dev' into add_taxpasta_merge
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2023-02-16 15:07:51 +01:00 |
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sofstam
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de6a4214ef
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Add taxpasta_merge to taxprofiler
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2023-02-16 14:29:52 +01:00 |
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James Fellows Yates
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7dfcdd015b
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Re-add the 'native' combined kaiju output
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2023-02-16 14:02:13 +01:00 |
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James Fellows Yates
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79b4db9a34
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Move kaiju2table to profiling
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2023-02-16 13:39:05 +01:00 |
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James Fellows Yates
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ce1118930d
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Resource optimisation
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2023-02-09 13:33:39 +01:00 |
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James Fellows Yates
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cc7d219267
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Revert "optimisation for single-cpu processes"
This reverts commit a731669b8e .
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2023-02-09 13:32:29 +01:00 |
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James Fellows Yates
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a731669b8e
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optimisation for single-cpu processes
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2023-02-09 13:31:57 +01:00 |
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James A. Fellows Yates
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45ac6fedc2
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Merge pull request #237 from nf-core/bracken-params
Support Kraken and Bracken db_params in database sheet
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2023-02-09 10:59:27 +01:00 |
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James A. Fellows Yates
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70eb84b8d5
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2023-02-09 08:01:52 +01:00 |
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James Fellows Yates
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18886c0cbc
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Start trying a different method with maps in profiling
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2023-02-07 15:51:25 +01:00 |
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James Fellows Yates
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059cd17114
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Fix exporting of mapped/unmapped reads for consistency across both short and long reads
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2023-02-07 11:43:40 +01:00 |
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sofstam
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5363274867
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Add some last documentation
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2023-02-02 13:58:48 +01:00 |
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James Fellows Yates
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7ce55a99e8
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Fix linting
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2023-02-02 13:08:16 +01:00 |
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James A. Fellows Yates
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c4e366d47d
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Add full test data and documentation of the test data
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2023-02-02 11:59:26 +01:00 |
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James A. Fellows Yates
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1d7da61801
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Merge pull request #223 from nf-core/multiqc-tweaks
MultiQC Tweaks after full-test experiments
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2023-01-30 11:25:28 +01:00 |
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James A. Fellows Yates
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098ec087c9
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Merge pull request #217 from nf-core/combine-kreports-fix [skip ci]
Dont fail on divide by 0 errors on centrifuge
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2023-01-25 13:48:06 +01:00 |
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James Fellows Yates
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a993300099
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Tweaks to MultiQC based on full test experiments
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2023-01-24 15:06:42 +01:00 |
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James Fellows Yates
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e7d7affcd0
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Pick up Kraken2 files correctly
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2023-01-24 14:44:14 +01:00 |
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Moritz E. Beber
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40f1e7b27a
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fix: correct pattern to publish minimap2 index
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2023-01-24 14:15:51 +01:00 |
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James Fellows Yates
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1c820f21b3
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Dont fail on divide by 0 errors on centrifuge
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2023-01-20 17:53:55 +01:00 |
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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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