James A. Fellows Yates
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169c7437c8
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Left over from template merge
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2022-09-01 16:28:05 +02:00 |
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James A. Fellows Yates
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2ca837a4a3
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Merge pull request #115 from nf-core/json-schema
Add documentation for all parameters JSON schema (and other minor usage documentation tweaks)
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2022-08-31 15:19:07 +02:00 |
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James Fellows Yates
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3eb136ec3c
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Merge branch 'dev' into json-schema
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2022-08-31 12:55:49 +02:00 |
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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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394084a31b
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Merge pull request #113 from nf-core/filtlong-in-tests
Improve longread QC parameters
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2022-08-31 09:36:12 +02:00 |
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James A. Fellows Yates
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5274ac57af
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Update .prettierignore
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2022-08-31 09:24:24 +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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James Fellows Yates
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0107330d92
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Clarify specifying output parameters in database db_params column
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2022-08-31 08:34:57 +02:00 |
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James Fellows Yates
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806208c4b1
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Final tweaks to schema, and add a couple of notes for dev guidance on where their various --save_reads parameters are injected
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2022-08-31 08:30:26 +02:00 |
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James Fellows Yates
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acd0570b4a
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Finalise first pass of nextflow json documentation
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2022-08-31 07:56:39 +02:00 |
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James Fellows Yates
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bdcae4f934
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More docs and tweat to usage.md
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2022-08-30 16:04:05 +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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c2eaa3f6b0
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Prettier
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2022-08-30 14:33:40 +02:00 |
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James Fellows Yates
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d19a473c59
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Merge branch 'filtlong-in-tests' into json-schema
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2022-08-30 14:33:19 +02:00 |
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James A. Fellows Yates
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f393d1fe91
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Update nextflow.config
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2022-08-30 14:21:20 +02:00 |
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James Fellows Yates
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5552c264b9
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Remove now unnecessary input validation
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2022-08-30 14:14:01 +02:00 |
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James Fellows Yates
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8917e29e35
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Fix accidental overly zelous search-and-replace
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2022-08-30 14:11:48 +02:00 |
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James Fellows Yates
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3f8f32cba8
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Make longread quality ftilering opt out
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2022-08-30 14:08:05 +02:00 |
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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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95ad380173
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Turn of length filtering by default for short read (to match opt in for longread qc)
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2022-08-30 14:01:52 +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 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 Fellows Yates
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d6d51e0e43
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Start work on reordering json schema parameters
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2022-08-24 15:23:51 +02:00 |
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James A. Fellows Yates
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1821496a49
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Merge pull request #90 from nf-core/samplesheet-check-improvement
Make check_samplesheet.py compatible with nf-core/fetchngs
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2022-08-23 15:57:59 +01:00 |
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James A. Fellows Yates
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22e03e73e3
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Merge pull request #111 from nf-core/minimal-test
Add test_nothing config profile for very minimal testing
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2022-08-23 15:57:52 +01:00 |
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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 A. Fellows Yates
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4315141c5f
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Update bin/check_samplesheet.py
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-08-23 15:44:53 +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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James A. Fellows Yates
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3e24f491b5
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Merge pull request #106 from nf-core/porechop-log
Add emitting porechop logs to multiqc and fix collection of others
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2022-07-29 10:58:12 +02:00 |
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James A. Fellows Yates
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f48b22d615
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Apply suggestions from code review
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2022-07-29 09:52:49 +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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06298e867c
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Merge pull request #105 from genomic-medicine-sweden/diamond-update
Update the dev branch with the DIAMOND module update
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2022-07-28 17:21:59 +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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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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Sofia Stamouli
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ba928af5ab
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Merge pull request #110 from genomic-medicine-sweden/update_centrifuge_kreport
Update centrifuge kreport
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2022-07-28 10:36:30 +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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sofstam
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9bc45a3f24
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Update centrifuge/kreport
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2022-07-27 14:44:26 +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 Fellows Yates
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25bcc0798d
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Start work on multiQC config with distinguishing Kraken/Centrifuge
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2022-07-27 14:40:17 +02:00 |
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nf-core-bot
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a3bcf8665a
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[automated] Fix linting with Prettier
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2022-07-26 18:47:40 +00:00 |
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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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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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fdd9a3bc4d
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Merge pull request #107 from nf-core/fix-multiqc-mixing
Fix MultiQC mixing
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2022-07-26 12:38:52 +02:00 |
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James A. Fellows Yates
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65b0af9a8b
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Fix profiling channels
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2022-07-26 08:53:43 +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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