James A. Fellows Yates
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cf8ad96771
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Update subworkflows/local/profiling.nf
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2022-12-02 15:09:08 +01:00 |
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James Fellows Yates
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ab42f6b662
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wteak message
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2022-12-02 12:49:00 +01:00 |
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James Fellows Yates
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a3cd188b1f
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Merge branch 'sep-krakenuniq-test' of github.com:nf-core/taxprofiler into sep-krakenuniq-test
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2022-12-02 12:48:18 +01:00 |
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James Fellows Yates
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de74e4f727
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Fix centrifuge warning, filter out long reads from Brakcen, add some caveat docs to usage.md
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2022-12-02 12:47:14 +01:00 |
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James A. Fellows Yates
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a34b240dfc
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Merge pull request #174 from nf-core/malt-update
Update MALT
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2022-12-01 13:58:30 +01:00 |
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James Fellows Yates
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d7fbe55849
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Add KU to the test profiles and add id to KU processes
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2022-11-29 14:19:01 +01:00 |
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Moritz E. Beber
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ddcf38de22
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refactor: make mappings explicit
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2022-11-29 10:14:20 +01:00 |
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James Fellows Yates
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9feb6c2db6
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Update MALT
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2022-11-24 14:44:04 +01:00 |
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James Fellows Yates
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06659af777
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Remove flatten
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2022-11-22 13:36:40 +01:00 |
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James Fellows Yates
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ebfc84e235
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Does the grouping work if we have meta?
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2022-11-22 13:26:54 +01:00 |
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James Fellows Yates
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21759807f7
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Does flatten work?
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2022-11-22 12:48:54 +01:00 |
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James Fellows Yates
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3102e40052
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dump teh db
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2022-11-22 12:46:26 +01:00 |
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James Fellows Yates
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557f2a4d96
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Extra dump
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2022-11-22 12:26:46 +01:00 |
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James Fellows Yates
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5caebcc6ab
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Append to correct db
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2022-11-22 12:21:59 +01:00 |
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James Fellows Yates
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52fc00802b
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Correct meta name for db meta
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2022-11-22 12:19:56 +01:00 |
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James Fellows Yates
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b8937748d3
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Fix meta.id isssue
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2022-11-22 12:18:52 +01:00 |
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James Fellows Yates
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db334c5185
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Fix missing info
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2022-11-22 12:17:08 +01:00 |
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James Fellows Yates
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0f298dca43
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group krakenuniq reads by pairs or single end
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2022-11-22 12:13:08 +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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21a76c2449
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Fix cardinality issue
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2022-11-03 14:56:26 +01:00 |
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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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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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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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Moritz E. Beber
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ca7dc308cb
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Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-10-21 16:36:35 +02:00 |
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Moritz E. Beber
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385507ec6f
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refactor: use tool name 'bracken' only
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2022-10-21 10:03:36 +02:00 |
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Moritz E. Beber
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b73b479860
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refactor: handle combined kraken2+bracken tool column
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2022-10-19 16:21:36 +02:00 |
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Moritz E. Beber
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563b34c9c3
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refactor: rename process to kraken2
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2022-10-14 14:48:27 +02:00 |
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Moritz E. Beber
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95621ebd8a
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fix: include local module
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2022-10-14 14:47:08 +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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Moritz E. Beber
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f5af9fd939
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fix: adjust import paths to re-organization
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2022-10-05 13:40:43 +02:00 |
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James Fellows Yates
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21ae9d85c3
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Ensure merge metaphlan3 tables happens on per database basis
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2022-09-15 12:29:54 +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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d11257b330
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Module update
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2022-09-08 08:08:36 +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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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 Fellows Yates
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d4af88e3ff
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Make kaiju parameter clearer for documentation purpses and update documentation
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2022-08-25 15:50:28 +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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James Fellows Yates
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873a13e028
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Merge remote-tracking branch 'origin/dev' into porechop-log
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2022-07-29 09:51:34 +02:00 |
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Mahwash Jamy
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49487593e2
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Merge branch 'nf-core:dev' into diamond-update
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2022-07-28 15:48:59 +02:00 |
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sofstam
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cecbb41f88
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Update centrifuge/kreport
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2022-07-27 14:42:35 +02:00 |
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James A. Fellows Yates
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9d2be68fb8
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Merge branch 'dev' into centrifuge_mqc
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2022-07-26 18:01:30 +00:00 |
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James A. Fellows Yates
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1ef0975736
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Merge branch 'dev' into porechop-log
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2022-07-26 18:00:28 +00:00 |
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James A. Fellows Yates
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3054dea7c2
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Get multiqc input working
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2022-07-26 08:41:06 +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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139cf0d6aa
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Fix
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2022-07-26 10:12:33 +02:00 |
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James Fellows Yates
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255afee4c7
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Re-add the collects
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2022-07-19 17:10:10 +02:00 |
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Mahwash Jamy
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811ded38af
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Update subworkflows/local/profiling.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-07-19 16:44:48 +02:00 |
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James A. Fellows Yates
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8d7ddb5847
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Apply suggestions from code review
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2022-07-19 16:30:13 +02:00 |
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