James Fellows Yates
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606ffc0eb1
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Remove platform specificity for MALT
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2023-01-20 13:40:59 +01:00 |
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James Fellows Yates
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e5c6db96c8
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update all modules to make templaite compatible
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2022-12-23 17:23:05 +01:00 |
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Sofia Stamouli
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41c1ae9d1a
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Commit suggestion
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-12-23 12:20:37 +01:00 |
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sofstam
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85906ab1cb
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Optional untar on dbs
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2022-12-23 11:25:57 +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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James Fellows Yates
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577da7e835
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Remove .first() as the module only executes once anyway and we get a ugly warning
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2022-12-20 13:59:14 +01:00 |
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James Fellows Yates
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11db981a88
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minor fixes
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2022-12-20 13:55:15 +01:00 |
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James A. Fellows Yates
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7709245874
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Update subworkflows/local/input_check.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-12-20 13:54:05 +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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7c66968fef
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More comments
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2022-12-12 11:04:21 +01:00 |
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James Fellows Yates
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460f3ca157
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Add database sheet validation
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2022-12-12 11:03:40 +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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24e5bc5410
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refactor: use shorter and more explicit syntax
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2022-12-04 21:54:10 +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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0dccfddc24
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Switch order back
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2022-12-03 21:38:25 +01:00 |
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James A. Fellows Yates
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cf8ad96771
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Update subworkflows/local/profiling.nf
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2022-12-02 15:09:08 +01:00 |
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James Fellows Yates
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ab42f6b662
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wteak message
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2022-12-02 12:49:00 +01:00 |
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James Fellows Yates
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a3cd188b1f
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Merge branch 'sep-krakenuniq-test' of github.com:nf-core/taxprofiler into sep-krakenuniq-test
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2022-12-02 12:48:18 +01:00 |
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James Fellows Yates
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de74e4f727
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Fix centrifuge warning, filter out long reads from Brakcen, add some caveat docs to usage.md
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2022-12-02 12:47:14 +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 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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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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Moritz E. Beber
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ddcf38de22
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refactor: make mappings explicit
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2022-11-29 10:14:20 +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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sofstam
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481f90589c
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Apply review suggestions
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2022-11-23 09:08:22 +01:00 |
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sofstam
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30af26a8b3
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Include the mapped reads in samtools stats
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2022-11-22 16:50:50 +01:00 |
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James Fellows Yates
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06659af777
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Remove flatten
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2022-11-22 13:36:40 +01:00 |
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James Fellows Yates
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ebfc84e235
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Does the grouping work if we have meta?
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2022-11-22 13:26:54 +01:00 |
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James Fellows Yates
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21759807f7
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Does flatten work?
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2022-11-22 12:48:54 +01:00 |
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James Fellows Yates
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3102e40052
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dump teh db
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2022-11-22 12:46:26 +01:00 |
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James Fellows Yates
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557f2a4d96
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Extra dump
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2022-11-22 12:26:46 +01:00 |
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James Fellows Yates
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5caebcc6ab
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Append to correct db
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2022-11-22 12:21:59 +01:00 |
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James Fellows Yates
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52fc00802b
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Correct meta name for db meta
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2022-11-22 12:19:56 +01:00 |
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James Fellows Yates
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b8937748d3
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Fix meta.id isssue
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2022-11-22 12:18:52 +01:00 |
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James Fellows Yates
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db334c5185
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Fix missing info
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2022-11-22 12:17:08 +01:00 |
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James Fellows Yates
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0f298dca43
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group krakenuniq reads by pairs or single end
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2022-11-22 12:13:08 +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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James Fellows Yates
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461482d22a
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Try again wit hthe corret param
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2022-11-03 15:02:22 +01:00 |
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James Fellows Yates
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93f38b14a8
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Save report
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2022-11-03 15:01:00 +01:00 |
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James Fellows Yates
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21a76c2449
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Fix cardinality issue
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2022-11-03 14:56:26 +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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3faea8aac5
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Fix porechop conflict
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2022-11-01 17:34:37 +01:00 |
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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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ce611d6efd
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Add bowtie2 mapped reads
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2022-10-31 10:04:51 +01:00 |
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Sofia Stamouli
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f1778acf35
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Apply review suggestion
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2022-10-31 09:31:13 +01:00 |
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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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1bd6dbfe58
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Add samtools stats for long-reads
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2022-10-28 11:40:50 +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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08d61065e5
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Add adapterlist to AR2 subworkflow
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2022-10-27 12:23:27 +00:00 |
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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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Moritz E. Beber
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e658fab430
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fix: remove def
No idea why, must have something to do with scope.
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2022-10-27 11:50:47 +02:00 |
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Moritz E. Beber
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dd1a4ff158
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refactor: only combine same database name
[skip ci]
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2022-10-27 11:19:14 +02:00 |
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Mahwash Jamy
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86ca71cfd4
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include krakenuniq in profiling subworkflow
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2022-10-25 09:45:05 +00:00 |
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Sofia Stamouli
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8c3e80b6ea
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Add helptest to nextflow_schema,add versions to longread_preprocessing
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2022-10-25 11:13:26 +02:00 |
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Moritz E. Beber
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ca7dc308cb
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Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-10-21 16:36:35 +02:00 |
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Moritz E. Beber
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385507ec6f
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refactor: use tool name 'bracken' only
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2022-10-21 10:03:36 +02:00 |
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Sofia Stamouli
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511cb16a61
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Apply review suggestions
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2022-10-20 16:55:57 +02:00 |
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Moritz E. Beber
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8deb7757d8
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fix: remove Bracken from standardise reports
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2022-10-19 16:21:57 +02:00 |
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Moritz E. Beber
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b73b479860
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refactor: handle combined kraken2+bracken tool column
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2022-10-19 16:21:36 +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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48b00b7d62
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refactor: create standardized Bracken reports
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2022-10-17 17:33:24 +02:00 |
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Moritz E. Beber
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563b34c9c3
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refactor: rename process to kraken2
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2022-10-14 14:48:27 +02:00 |
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Moritz E. Beber
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95621ebd8a
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fix: include local module
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2022-10-14 14:47:08 +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 Fellows Yates
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56bae85755
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Remove necessity of patch
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2022-10-11 12:38:18 +02:00 |
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Moritz E. Beber
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180cac0395
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fix: adapt to new samtools/view input
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2022-10-05 13:49:35 +02:00 |
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Moritz E. Beber
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f5af9fd939
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fix: adjust import paths to re-organization
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2022-10-05 13:40:43 +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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87edc4569c
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Move to a function
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2022-09-27 15:46:17 +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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1584d6fc51
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Update workflows/taxprofiler.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-09-19 10:43:04 -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 A. Fellows Yates
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f43c54317c
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Update subworkflows/local/standardisation_profiles.nf
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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2022-09-16 15:20:47 +02:00 |
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James Fellows Yates
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c5cc21d29e
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Update motus merge module to remove unused channel
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2022-09-16 10:25:24 +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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Rafal Stepien
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768f9980d8
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Add pep_input_base_dir to workflow. Just need to update modules
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2022-09-15 12:31:49 -04:00 |
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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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21ae9d85c3
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Ensure merge metaphlan3 tables happens on per database basis
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2022-09-15 12:29:54 +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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d11257b330
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Module update
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2022-09-08 08:08:36 +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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8456f934ed
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Update subworkflows/local/visualization_krona.nf
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2022-09-02 16:15:46 +02:00 |
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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 Fellows Yates
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d19a473c59
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Merge branch 'filtlong-in-tests' into json-schema
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2022-08-30 14:33:19 +02:00 |
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James Fellows Yates
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3f8f32cba8
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Make longread quality ftilering opt out
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2022-08-30 14:08:05 +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 Fellows Yates
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d4af88e3ff
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Make kaiju parameter clearer for documentation purpses and update documentation
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2022-08-25 15:50:28 +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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James A. Fellows Yates
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f48b22d615
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Apply suggestions from code review
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2022-07-29 09:52:49 +02:00 |
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James Fellows Yates
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873a13e028
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Merge remote-tracking branch 'origin/dev' into porechop-log
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2022-07-29 09:51:34 +02:00 |
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Mahwash Jamy
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49487593e2
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Merge branch 'nf-core:dev' into diamond-update
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2022-07-28 15:48:59 +02:00 |
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sofstam
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cecbb41f88
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Update centrifuge/kreport
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2022-07-27 14:42:35 +02:00 |
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