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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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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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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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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Moritz E. Beber
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60e369aa5c
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fix: set default run bracken to false
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2022-10-21 10:47:51 +02:00 |
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Moritz E. Beber
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c7c7a7f678
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refactor: change Bracken prefix to be more specific
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2022-10-19 16:20:09 +02:00 |
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Sofia Stamouli
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7881ba9aef
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Fix the amount of left-padding spaces
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2022-10-18 17:50:49 +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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767663d975
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chore: add Bracken to test configs
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2022-10-14 12:18:55 +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 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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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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9349346864
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Remove --pep parameter and leave just --input
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2022-09-16 10:14:01 -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 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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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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19a195ed14
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Append profiler to resulting file
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2022-09-15 12:30:39 +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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fc26948950
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Fix MultiQC
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2022-09-08 12:49:38 +02:00 |
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James Fellows Yates
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832d981976
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Don't have per sample directory as unnecessary if file names are unique with the db in them
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2022-09-07 12:22:17 +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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dd194f3f47
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Fix mOTUs CI and old param warn
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2022-09-04 15:01:58 +00:00 |
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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 A. Fellows Yates
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f7b7fd63a4
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Merge pull request #114 from nf-core/nf-core-template-merge-2.5
Important! Template update for nf-core/tools v2.5
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2022-08-31 10:28:14 +02:00 |
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James A. Fellows Yates
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28d8d3f8fb
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Merge branch 'dev' into nf-core-template-merge-2.5
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2022-08-31 09:16:34 +02:00 |
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nf-core-bot
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6dfca81761
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Template update for nf-core/tools version 2.5
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2022-08-30 13:43:03 +00:00 |
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James Fellows Yates
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afba604e8b
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Make everything within opt-out, once QC is opted-in
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2022-08-30 14:04:34 +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 A. Fellows Yates
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a3055bf6da
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Update conf/test_nothing.config
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2022-08-23 15:48:02 +02:00 |
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James Fellows Yates
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e6c7939305
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Add test_nothing config profile for minimal testing
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2022-08-23 14:37:01 +02:00 |
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James Fellows Yates
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a97bb69cd2
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Prettier
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2022-08-23 14:24:57 +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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mjamy
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5cdf5e958a
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Updated modules.config to add 'log' in diamond config
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2022-07-28 16:08:15 +02:00 |
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sofstam
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71cf32cc6a
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Add error strategy for centrifuge/kreport
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2022-07-28 08:54:32 +02:00 |
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James A. Fellows Yates
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65ae82efc4
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Define separte krakena nd centrigfue modules
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2022-07-26 18:37:33 +00:00 |
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James A. Fellows Yates
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e76b299705
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Start working getting kraken and centrifuge working in MQC
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2022-07-26 08:18:54 +00:00 |
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James Fellows Yates
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a0ee82bf43
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Add motus/merge and biom support
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2022-07-12 11:39:26 +02:00 |
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James A. Fellows Yates
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8082c7d108
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Merge pull request #97 from nf-core/malt-to-krona
Add Krona support for MALT
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2022-07-05 15:17:52 +02:00 |
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James A. Fellows Yates
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26e31c782d
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Merge branch 'dev' into motus
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2022-07-04 13:14:42 +02:00 |
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James Fellows Yates
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447b8f0905
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Get fixed Krona module and add Krona taxonomy to test profile
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2022-07-01 17:21:19 +02:00 |
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James Fellows Yates
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02c06b9f7b
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Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file
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2022-06-30 18:33:11 +02:00 |
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069370db86
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Add unclassified and verbose flags to kaiju2krona
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2022-06-28 09:00:42 -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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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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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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