James A. Fellows Yates
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727291999b
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Merge branch 'dev' into nf-core-template-merge-2.8
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1 year ago |
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James Fellows Yates
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44286bf96d
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Improve mOTUS database input desciption
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1 year ago |
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James A. Fellows Yates
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bca6e645a8
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Merge branch 'dev' into nf-core-template-merge-2.8
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1 year ago |
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nf-core-bot
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ac60d66956
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Template update for nf-core/tools version 2.8
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1 year ago |
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James A. Fellows Yates
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0245c4880b
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Merge branch 'dev' into final-reads-saving
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1 year ago |
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James A. Fellows Yates
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105bac7bb9
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Apply suggestions from code review
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1 year ago |
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James A. Fellows Yates
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ee031ebf91
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Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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1 year ago |
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James Fellows Yates
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3f34603c00
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Prettier
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1 year ago |
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James Fellows Yates
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ce97a1124e
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Add final documentation
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1 year ago |
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James Fellows Yates
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6895e45768
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Fix a few conditional bugs and related
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1 year ago |
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sofstam
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102d53bd75
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Subsitute samtools/bam2fq with samtools/fastq
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1 year ago |
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James Fellows Yates
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b0939c3ae9
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Standardised taxon table and mOTU database docs improvement
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1 year ago |
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James A. Fellows Yates
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7f6e162e1c
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Update docs/output.md
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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1 year ago |
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James Fellows Yates
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e49668005f
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Update docs based on feedback and add missing results directories
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1 year ago |
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James A. Fellows Yates
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91a7a03f48
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Apply suggestions from code review
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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1 year ago |
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James Fellows Yates
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a2a1b9cbf0
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Phrasing tweak
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1 year ago |
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James Fellows Yates
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4938549d65
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Clarify some documentation
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1 year ago |
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James A. Fellows Yates
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f0f89eb082
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Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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1 year ago |
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James Fellows Yates
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74a5343524
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Add taxpasta to tubemap
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1 year ago |
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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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1 year ago |
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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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1 year ago |
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Sofia Stamouli
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d454ceed86
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Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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1 year ago |
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Sofia Stamouli
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1aef73cda8
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Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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1 year ago |
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sofstam
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2f0c68a833
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Last review suggestions
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1 year ago |
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sofstam
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78d7001bea
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Document the taxonomy parameters
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1 year ago |
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sofstam
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211b5f3a68
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Apply review suggestions
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1 year ago |
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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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1 year ago |
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sofstam
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604df56fdb
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Add a description about the files used by taxpasta
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1 year ago |
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sofstam
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08bfa6a1a7
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Apply review suggestions for docs
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1 year ago |
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sofstam
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27b7171b96
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Apply review suggestions
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1 year ago |
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sofstam
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c9b521234b
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Prettier for docs
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1 year ago |
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sofstam
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dad64a688d
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Add documentation for taxpasta module
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1 year ago |
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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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1 year ago |
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James A. Fellows Yates
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4e818efe6d
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Update docs/output.md
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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1 year ago |
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James Fellows Yates
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79b4db9a34
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Move kaiju2table to profiling
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1 year ago |
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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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1 year ago |
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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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1 year ago |
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James Fellows Yates
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b3837cce5b
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Relax strictness so can supply empty db_params but block if only single parameter with out ;
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1 year ago |
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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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1 year ago |
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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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1 year ago |
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sofstam
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4123e06981
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Apply last review suggestions
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1 year ago |
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sofstam
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3e2b181182
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Apply review suggestions
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1 year ago |
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Sofia Stamouli
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ffc884b542
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Merge branch 'nf-core:dev' into documentation
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1 year ago |
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James A. Fellows Yates
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b4f88a29ce
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Update docs/usage.md [skip ci]
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1 year ago |
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James A. Fellows Yates
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11a8624b39
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Add warning about database parameters [skip ci]
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1 year ago |
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sofstam
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5363274867
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Add some last documentation
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1 year ago |
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James Fellows Yates
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932dc12fb1
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Add list of expected tools in MultiQC report [skip ci]
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1 year ago |
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James Fellows Yates
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52907dcc26
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Prettier
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1 year ago |
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James A. Fellows Yates
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b4d01ac226
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Formatting tweaks
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1 year ago |
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sofstam
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366745bdbe
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Prettier in usage
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1 year ago |