sofstam
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c47b9e55fa
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Mix reads in emit
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2023-04-04 18:01:02 +02:00 |
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sofstam
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8745fc625c
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Correct output file from samtools/fastq
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2023-03-29 15:36:20 +02:00 |
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sofstam
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102d53bd75
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Subsitute samtools/bam2fq with samtools/fastq
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2023-03-23 15:30:07 +01:00 |
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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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2023-03-12 08:35:45 +01:00 |
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James A. Fellows Yates
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5e400c8c89
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Apply suggestions from code review
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2023-03-11 20:06:59 +01:00 |
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Moritz E. Beber
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bb7323e25d
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fix: restore setting id on FASTQ meta
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2023-03-11 11:34:47 +01:00 |
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Moritz E. Beber
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7104b12e3b
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Update subworkflows/local/longread_preprocessing.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2023-03-11 11:28:42 +01:00 |
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Moritz E. Beber
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fa1c779536
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fix: insert id key again
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2023-03-11 11:28:42 +01:00 |
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Moritz E. Beber
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246da8a7b0
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chore: remove fixme comments
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2023-03-11 11:28:42 +01:00 |
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Moritz E. Beber
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7c1133efb8
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add more comments and slight style changes
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2023-03-11 11:28:42 +01:00 |
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Moritz E. Beber
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5380bc18ec
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fix: channels should match 1:1 without remaining elements
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2023-03-11 11:28:42 +01:00 |
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Moritz E. Beber
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07db3c93e2
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style: use map addition instead of cloning
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2023-03-11 11:28:42 +01:00 |
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Moritz E. Beber
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d17dce5590
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style: use subMap and early returns
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2023-03-11 11:28:42 +01:00 |
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Moritz E. Beber
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0bcea6c993
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style: use parameter for branch closure
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2023-03-11 11:28:42 +01:00 |
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Moritz E. Beber
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b90433f3c2
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style: use parameters for filter closure
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2023-03-11 11:28:42 +01:00 |
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Moritz E. Beber
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aa2410a871
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style: use named parameters for closure
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2023-03-11 11:28:42 +01:00 |
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Moritz E. Beber
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c2ad421051
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refactor: simplify DB validation
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2023-03-11 11:28:42 +01:00 |
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James Fellows Yates
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98bc6910d5
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Update authors and remove left over comment
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2023-03-07 11:47:54 +01:00 |
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James Fellows Yates
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6e64c2b5a9
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Fix copy paste error
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2023-03-06 10:50:36 +01:00 |
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James Fellows Yates
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735212c9ee
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Fix the non-updated KAIJU2TABLE name
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2023-03-06 10:47:36 +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
|
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 A. Fellows Yates
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32c0d8d6a5
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Fix KrakenUniq Taxpasta issue
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2023-02-22 08:24:48 +01:00 |
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sofstam
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90aa7551a9
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Fix the motus_versions
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2023-02-20 14:27:57 +01:00 |
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sofstam
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3fa1b0c17d
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Remove standardised_tables
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2023-02-20 13:48:04 +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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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
|
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 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
|
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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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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2023-02-08 15:44:37 +01:00 |
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James Fellows Yates
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fe3d42ffd7
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Make bracken db_params be a semi-colon separate list to allow kraken and bracken parameters
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2023-02-08 13:34:36 +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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James A. Fellows Yates
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47efd193cb
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Merge pull request #219 from nf-core/allow-targz-motus [skip ci]
Allow all tool's databases to be provided as `.tar.gz` files
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2023-01-25 13:48:43 +01:00 |
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James A. Fellows Yates
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4289e1f901
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Remove metaphlan3 nanopore filter as _sometimes_ it can work
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2023-01-24 15:42:14 +01:00 |
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James A. Fellows Yates
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c765b3f0bc
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Merge branch 'dev' into allow-targz-motus
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2023-01-24 15:20:29 +01:00 |
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James A. Fellows Yates
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00178d3431
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Merge pull request #221 from nf-core/metaphlan3-filter-nanopore
Filter out nanopore data prior Metaphlan3
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2023-01-24 14:39:02 +01:00 |
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James Fellows Yates
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14826d5205
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Separate conditions, remove some left-over dumps
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2023-01-24 13:20:58 +01:00 |
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James Fellows Yates
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0358489be0
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Remove metaphlan profiling for nanopore as it appears to always result in 100% unclassified
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2023-01-24 13:05:52 +01:00 |
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James A. Fellows Yates
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6eafcc6499
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Try Moritz's trick, assuming validate_db_rows already checks for tool name validity
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2023-01-24 12:43:34 +01:00 |
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James Fellows Yates
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4df3409f4a
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Merge branch 'dev' of github.com:nf-core/taxprofiler into allow-targz-motus
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2023-01-24 11:50:28 +01:00 |
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James Fellows Yates
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9205831273
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Start adding filter for long read and MP3
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2023-01-24 11:50:10 +01:00 |
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James Fellows Yates
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1a148c5d49
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Remove double If and format for readability
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2023-01-24 10:48:23 +01:00 |
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James A. Fellows Yates
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d56e3133f9
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Allow databases of all tools to arrive as tar.gz
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2023-01-24 10:45:01 +01:00 |
|
James Fellows Yates
|
606ffc0eb1
|
Remove platform specificity for MALT
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2023-01-20 13:40:59 +01:00 |
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James Fellows Yates
|
e5c6db96c8
|
update all modules to make templaite compatible
|
2022-12-23 17:23:05 +01:00 |
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