James Fellows Yates
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082093f3de
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Prettier
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2022-04-10 06:44:10 +02:00 |
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James Fellows Yates
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ecf0eea4f9
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Move profiling to subworkflow and standardise outputs
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2022-04-10 06:43:30 +02:00 |
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sofstam
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606e5da7d5
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Check if PR works with centrifuge/centrifuge module
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2022-04-07 16:13:17 +02:00 |
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James Fellows Yates
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98f082d7b6
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Fix mistake in previous upstream merge with AR2 output channel for settings file
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2022-04-05 13:17:54 +02:00 |
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James Fellows Yates
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5b9355725d
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Whoops
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2022-04-05 13:14:06 +02:00 |
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James Fellows Yates
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245a4d1f5d
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Fix MQC staging and remove debugging dump
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2022-04-05 13:08:44 +02:00 |
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James A. Fellows Yates
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3d662d2e06
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Merge branch 'dev' into complexity-filter-bbduk
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2022-04-04 21:19:36 +02:00 |
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sofstam
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d897c922b2
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Add centrifuge classificatioN
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2022-04-04 13:51:51 +02:00 |
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James Fellows Yates
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469e4f3682
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Remove remaining debugging .dumps(
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2022-04-02 17:07:30 +02:00 |
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James Fellows Yates
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b055df5ea0
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Add bbduk complexity (entropy-based) filtering
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2022-04-02 17:02:05 +02:00 |
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Moritz E. Beber
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996b3f4912
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fix: correct the input shape to metaphlan3
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2022-04-02 15:00:26 +02:00 |
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Moritz E. Beber
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a425a322f2
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refactor: make metaphlan3 run in workflow
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2022-04-02 14:59:44 +02:00 |
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Moritz E. Beber
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69db920610
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feat: include metaphlan3 in workflow
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2022-04-02 14:59:44 +02:00 |
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James Fellows Yates
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93aaa9eeac
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Clean up AdapterRemoval and remove all debugging dumps
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2022-04-01 21:36:22 +02:00 |
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James Fellows Yates
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94e5cfef4a
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Filter long reads for MALT, bump cpus for FastQC for minigut to pass
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2022-03-28 18:20:10 +02:00 |
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James Fellows Yates
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231253227c
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Remove run merging for now due to complexity
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2022-03-28 16:38:10 +02:00 |
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James Fellows Yates
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ee53283696
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Debugging comment
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2022-03-28 09:13:05 +02:00 |
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James Fellows Yates
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8dc9e583ad
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Debugging run merging
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2022-03-27 09:30:23 +02:00 |
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James A. Fellows Yates
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e6e8ed7cc9
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Add some debugging notes
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2022-03-26 20:54:50 +00:00 |
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James Fellows Yates
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120382f51d
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Fix input channels to kraken2
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2022-03-26 06:45:16 +01:00 |
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sofstam
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37a70dc3e3
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Merge branch 'dev' into classification_centrifuge
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2022-03-25 16:18:35 +01:00 |
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James Fellows Yates
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4e93abc7c0
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Add read improved read preprocessing
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2022-03-25 14:58:06 +01:00 |
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James Fellows Yates
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cc9368ee52
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Prettier linting and update schema
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2022-03-24 15:35:09 +01:00 |
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James A. Fellows Yates
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edce6603ef
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Merge branch 'dev' into nf-core-template-merge-2.3.2
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2022-03-24 14:10:58 +01:00 |
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sofstam
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3ff54e620e
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Add centrifuge classification
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2022-03-24 13:02:25 +01:00 |
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nf-core-bot
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6b939e6728
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Template update for nf-core/tools version 2.3.1
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2022-03-23 13:57:56 +00:00 |
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James Fellows Yates
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81bfb629ca
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Add working basic test to begin
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2022-03-21 20:28:09 +01:00 |
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James Fellows Yates
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8012998542
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Make parameter naming more consistent for clipmerge
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2022-03-21 19:52:50 +01:00 |
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ljmesi
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f6fe26de46
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Rename shortread subworkflow to be more consistent
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2022-03-21 18:25:56 +01:00 |
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ljmesi
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c97de32434
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Make adapter and quality trimming optional
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2022-03-21 18:17:08 +01:00 |
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ljmesi
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582aaa105f
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Include long reads preprocessing subworkflow
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2022-03-18 15:12:07 +01:00 |
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Lauri Mesilaakso
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0936b9b28e
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Update workflows/taxprofiler.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-03-18 14:18:38 +01:00 |
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ljmesi
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c8e49c56f4
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Perform fastqc on nanopore reads before trimming
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2022-03-18 13:47:44 +01:00 |
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James A. Fellows Yates
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ac77676d2b
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Merge branch 'dev' into nf-core-template-merge-2.3
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2022-03-17 13:11:34 +01:00 |
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nf-core-bot
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699d26b149
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Template update for nf-core/tools version 2.3
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2022-03-15 21:05:37 +00:00 |
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James Fellows Yates
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e39c6a8ccb
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Fix MALT multiqc report clash
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2022-03-03 18:04:03 +01:00 |
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James Fellows Yates
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2c183ed2ed
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Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue)
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2022-03-03 17:42:02 +01:00 |
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James Fellows Yates
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278f5605ca
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Added database preparation and final channel for profiling
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2022-02-19 12:36:08 +01:00 |
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James Fellows Yates
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cf55cc592c
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Get skeleton read processing to input for profiling
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2022-02-18 16:51:01 +01:00 |
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James Fellows Yates
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12e7b428f2
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initial template build from nf-core/tools, version 2.2
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2022-02-18 07:55:14 +01:00 |
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