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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79dd3930bb
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Add samtools to README
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2022-11-03 16:52:01 +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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c5e5696f84
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Fix parameter name
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2022-11-03 14:58:03 +01:00 |
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James Fellows Yates
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c03a21c770
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Merge branch 'add-krakenuniq-module' of github.com:mjamy/taxprofiler into add-krakenuniq-module
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2022-11-03 14:56:43 +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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nf-core-bot
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0c445759e4
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[automated] Fix linting with Prettier
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2022-11-03 13:42:39 +00:00 |
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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 Fellows Yates
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6459d8920f
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Linting!
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2022-11-03 14:05:43 +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 A. Fellows Yates
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62f45c8be7
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Update nextflow.config
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2022-11-03 10:03:27 +01:00 |
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James A. Fellows Yates
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24dc2a2cec
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-11-03 10:03:07 +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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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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aecf308840
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Update documentation for krakenuniq
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2022-10-31 16:41:35 +00:00 |
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Mahwash Jamy
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851016e497
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Update nextflow_scheme.json
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2022-10-31 16:17:40 +00:00 |
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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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074d3ec204
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Merge pull request #161 from genomic-medicine-sweden/samtools_stats
Add samtools stats for long-reads
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2022-10-31 10:59:37 +01:00 |
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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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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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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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10f7f9e5de
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Merge branch 'adapterremoval-fix' of https://github.com/nf-core/taxprofiler into adapterremoval-fix
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2022-10-27 12:23:52 +00:00 |
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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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nf-core-bot
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a402ee3be2
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[automated] Fix linting with Prettier
|
2022-10-27 12:20:08 +00:00 |
|
James A. Fellows Yates
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733d3dc8c5
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Apply suggestions from code review
|
2022-10-27 14:19:28 +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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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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Moritz E. Beber
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0de1ac5356
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docs: add Bracken reference
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2022-10-27 10:14:57 +02:00 |
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Sofia Stamouli
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63c260bfbc
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Merge pull request #148 from genomic-medicine-sweden/add_falco
Add Falco as an alternative to FastQC
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2022-10-25 12:40:26 +02:00 |
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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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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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Mahwash Jamy
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36e101a78b
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Install krakenuniq module
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2022-10-25 09:26:33 +00:00 |
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Sofia Stamouli
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de6816ec49
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Update nextflow_schema.json
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-10-25 11:19:16 +02:00 |
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Sofia Stamouli
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7b1a53b062
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Update nextflow_schema.json
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-10-25 11:19:08 +02:00 |
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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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nf-core-bot
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00038db634
|
[automated] Fix linting with Prettier
|
2022-10-25 08:51:58 +00:00 |
|
Sofia Stamouli
|
d3d4297ca9
|
Apply review suggestions
|
2022-10-24 16:28:07 +02:00 |
|
Moritz E. Beber
|
ca7dc308cb
|
Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2022-10-21 16:36:35 +02:00 |
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