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4de43040a3
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Switch to using raw classifications for Kaiju2Krona
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2022-06-28 09:00:41 -05:00 |
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821dd844d8
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Add Kaiju profile conversion to visualization workflow
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2022-06-27 09:23:20 -05:00 |
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5b80c7cab9
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Install KAIJU_KAIJU2KRONA
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2022-06-27 08:58:28 -05:00 |
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23fec89b06
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Add Krona chart creation for Centrifuge reports
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2022-06-27 08:52:29 -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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15ac8b39fa
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Add citation for Krona
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2022-06-27 08:25:48 -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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ad9bc4b7e9
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Add the visualization workflow to the main workflow
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2022-06-27 08:25:38 -05:00 |
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a40a442178
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Create VISUALIZATION_KRONA workflow to create Krona charts
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2022-06-27 08:22:47 -05:00 |
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5da8d5b741
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Install KRONA_KTIMPORTTEXT
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2022-06-14 10:34:34 -05:00 |
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87678c127b
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Add KRONA_CLEANUP process module
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2022-06-14 10:34:33 -05:00 |
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a84f693479
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Install KRAKENTOOLS_KREPORT2KRONA module
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2022-06-14 08:13:36 -05:00 |
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James A. Fellows Yates
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3dcda7446b
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Merge pull request #86 from nf-core/support-aligned-reads
Add working read alignment output for MALT/Kraken2/Centrifuge/DIAMOND
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2022-06-13 11:23:34 +02:00 |
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James Fellows Yates
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e0ad49ebc9
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Fix metadata manipulaton for malt
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2022-06-10 19:33:37 +02:00 |
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James A. Fellows Yates
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621b6a3d09
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Add comments about MALT id replacement and refactor for simplicity
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2022-06-10 11:27:51 +02:00 |
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James Fellows Yates
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6c6f5e0913
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Merge branch 'dev' of github.com:nf-core/taxprofiler into dev
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2022-06-09 08:21:51 +02:00 |
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James Fellows Yates
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ec13b8d608
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Remove support for uncompressed FASTQ files
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2022-06-09 08:21:48 +02:00 |
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James Fellows Yates
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800c0dd2aa
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Merge branch 'support-aligned-reads' of github.com:nf-core/taxprofiler into support-aligned-reads
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2022-06-09 08:16:01 +02:00 |
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James Fellows Yates
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490a8a8a84
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Remove dump
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2022-06-09 08:15:58 +02:00 |
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James A. Fellows Yates
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ebdd5683b2
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Apply suggestions from code review
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2022-06-03 22:33:48 +02:00 |
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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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James Fellows Yates
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d48b3be5a7
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Tweak DIAMOND save_reads message
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2022-06-03 13:55:17 +02:00 |
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James Fellows Yates
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3313b90453
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Fix JSOn schema
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2022-06-03 13:50:48 +02:00 |
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James A. Fellows Yates
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96fecb2bfc
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Merge branch 'dev' into support-aligned-reads
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2022-06-03 13:48:54 +02:00 |
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James A. Fellows Yates
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43ea8d299c
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Merge pull request #74 from nf-core/add-filtlong
Add initial longread QC filtering - requires filtlong module update
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2022-06-02 20:10:46 +02:00 |
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James Fellows Yates
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2838c136bd
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Prettier
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2022-06-02 12:51:39 +02:00 |
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James A. Fellows Yates
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c9581b1796
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Merge branch 'dev' into support-aligned-reads
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2022-06-02 12:45:29 +02:00 |
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James Fellows Yates
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d3d28da1b1
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Update after review
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2022-06-02 11:53:53 +02:00 |
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James A. Fellows Yates
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a196e0f628
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Merge branch 'dev' into add-filtlong
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2022-06-02 11:51:26 +02:00 |
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James A. Fellows Yates
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dfcaaae1fb
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Merge pull request #83 from ZandraFagernas/dev
Uploaded logo
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2022-06-02 11:31:32 +02:00 |
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James Fellows Yates
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fa70a413cb
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Use finally working filtlong module
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2022-05-31 21:12:09 +02:00 |
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James Fellows Yates
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16ec5bf74a
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Update parameter names
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2022-05-31 20:11:19 +02:00 |
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James Fellows Yates
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792e2d019b
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Fix merge error in schema
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2022-05-31 13:06:48 +02:00 |
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James Fellows Yates
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310ac6b450
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Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong
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2022-05-31 13:05:52 +02:00 |
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James Fellows Yates
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77da358e87
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Separate dark and light mode logos, add to README and add to MQC report
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2022-05-31 12:45:38 +02:00 |
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ZandraFagernas
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74b48f0919
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Add files via upload
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2022-05-28 13:29:24 +02:00 |
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James A. Fellows Yates
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ba75685550
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Merge pull request #81 from nf-core/nf-core-template-merge-2.4
Important! Template update for nf-core/tools v2.4
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2022-05-19 11:00:48 +01:00 |
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Moritz E. Beber
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a9fbe47992
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Merge branch 'dev' into nf-core-template-merge-2.4
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2022-05-19 08:42:28 +02:00 |
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nf-core-bot
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a560492353
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Template update for nf-core/tools version 2.4
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2022-05-16 10:22:38 +00:00 |
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James A. Fellows Yates
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63d9cbbdfd
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Merge pull request #80 from nf-core/activate-pipeline-specific-profiles
Activate institutional specific profiles
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2022-05-12 11:00:49 +02:00 |
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James A. Fellows Yates
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aca7bc439d
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Update nextflow.config
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2022-05-12 08:08:14 +01:00 |
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James A. Fellows Yates
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fd71b71929
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Merge pull request #79 from nf-core/fastp-complexity
Add FASTP complexity option
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2022-05-07 14:05:32 +02:00 |
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James A. Fellows Yates
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d67543503b
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-05-07 13:15:21 +02:00 |
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James Fellows Yates
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3fa2181f49
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Fix prinseq tool selection
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2022-05-07 06:15:15 +02:00 |
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James Fellows Yates
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0f651873dd
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Linting
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2022-05-07 06:12:24 +02:00 |
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James Fellows Yates
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47a5ae0cff
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Add FASTP complexity option
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2022-05-07 06:09:05 +02:00 |
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James Fellows Yates
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87a1d80519
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Add working output for Kraken2/Centrifuge/DIAMOND
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2022-05-07 05:22:35 +02:00 |
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James A. Fellows Yates
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e7b54801ed
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Merge pull request #75 from nf-core/improve-error-message
Only create profiler input channels when profiler activated
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2022-05-06 11:51:33 +02:00 |
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Lauri Mesilaakso
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e52a40cc9d
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Merge pull request #77 from genomic-medicine-sweden/add_nanopore_host_reads_removal_with_minimap2
Add nanopore host reads removal with minimap2
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2022-05-06 12:29:17 +03:00 |
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Lauri Mesilaakso
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02517733aa
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Update docs/usage.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-05-06 10:40:59 +02:00 |
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