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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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 A. Fellows Yates
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03e832954f
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Update subworkflows/local/shortread_adapterremoval.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-04-01 20:55:33 +02:00 |
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James A. Fellows Yates
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14f2b7bd84
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-04-01 15:34:05 +02:00 |
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James Fellows Yates
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dcda815bfb
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Add final adapterremoval options to match fastp functionality
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2022-04-01 09:50:08 +02:00 |
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James Fellows Yates
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c4c93bd59d
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Start working on adding adapterremoval
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2022-03-31 15:31:45 +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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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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622fafedc8
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Prempt centrifuge database untar crash
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2022-03-26 20:22:35 +00:00 |
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James A. Fellows Yates
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000f129dab
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Apply suggestions from code review
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2022-03-25 15:32:56 +01:00 |
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James Fellows Yates
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ede362dbf9
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Remove duplicate config and sync longread fastqc
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2022-03-25 15:28:30 +01:00 |
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James Fellows Yates
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b763bfa2c0
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More cleanup
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2022-03-25 15:26:57 +01:00 |
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James Fellows Yates
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0e6f7e2ca1
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Revert "Some more cleanup"
This reverts commit 7ddcb09a85 .
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2022-03-25 15:24:10 +01:00 |
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James Fellows Yates
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7ddcb09a85
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Some more cleanup
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2022-03-25 15:22:41 +01:00 |
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James Fellows Yates
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b5f5c75504
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Fix file header descriptions
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2022-03-25 15:21:52 +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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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 A. Fellows Yates
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3079f16861
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Merge branch 'dev' into database-untar
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2022-03-21 19:55:36 +01:00 |
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James Fellows Yates
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07eed435c6
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Replace set with explicity assignment
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2022-03-21 19:54:51 +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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5b1b48e59e
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Update subworkflow name to be more consistent
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2022-03-21 18:29:47 +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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James A. Fellows Yates
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631c115e10
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Adds PoC of untarring system
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2022-03-21 14:58:19 +00:00 |
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James Fellows Yates
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c7f022008c
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Start getting database prep ready
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2022-03-21 15:07:59 +01:00 |
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ljmesi
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1e42f1d9f2
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Add long read preprocessing subworkflow
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2022-03-18 15:10:44 +01:00 |
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ljmesi
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41b3d8db82
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Add nanopore channel
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2022-03-18 10:47:41 +01:00 |
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ljmesi
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0f0ed6cd46
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Fix function name
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2022-03-18 10:45:06 +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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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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