James A. Fellows Yates
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8c6f88d1b5
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Merge pull request #118 from nf-core/motus-test-fix
Fix mOTUs CI and old param warn
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2022-09-05 10:38:58 +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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d093de1bd0
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Merge pull request #117 from nf-core/fix-selector-warns
Fixes process selector warning
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2022-09-04 16:23:53 +02:00 |
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James A. Fellows Yates
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331231ea28
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Standardise CI execution
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2022-09-04 14:02:54 +00:00 |
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James A. Fellows Yates
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8456f934ed
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Update subworkflows/local/visualization_krona.nf
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2022-09-02 16:15:46 +02:00 |
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James Fellows Yates
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ef6fd002d4
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Merge branch 'dev' into fix-selector-warns
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2022-09-02 14:11:03 +02:00 |
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James A. Fellows Yates
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c9a7797682
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Merge pull request #116 from nf-core/nf-core-template-merge-2.5.1
Important! Template update for nf-core/tools v2.5.1
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2022-09-02 13:47:39 +02:00 |
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James Fellows Yates
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c3427e44b3
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Try with retries from sarek approach
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2022-09-02 12:24:29 +02:00 |
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James Fellows Yates
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3a33d81e80
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Black linting I hope
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2022-09-02 11:55:19 +02:00 |
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James Fellows Yates
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7917e1d656
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Synronise mOTUs CI setup
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2022-09-02 11:51:18 +02:00 |
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James Fellows Yates
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55d7919fa7
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Revert "Update ci.yml"
This reverts commit 176a0a6280.
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2022-09-02 11:48:57 +02:00 |
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James Fellows Yates
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c479714a5e
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Revert "Update ci.yml"
This reverts commit 61560cf065.
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2022-09-02 11:48:49 +02:00 |
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James Fellows Yates
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8fe7f8bf4b
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Revert "Fix final linting problems for template merge"
This reverts commit e64b3f85a4.
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2022-09-02 11:47:33 +02:00 |
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James A. Fellows Yates
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61560cf065
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Update ci.yml
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2022-09-02 10:12:27 +02:00 |
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James A. Fellows Yates
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176a0a6280
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Update ci.yml
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2022-09-02 10:06:20 +02:00 |
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James A. Fellows Yates
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e64b3f85a4
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Fix final linting problems for template merge
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2022-09-02 06:07:33 +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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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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8fff741f85
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Merge branch 'dev' into nf-core-template-merge-2.5.1
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2022-09-01 16:26:45 +02:00 |
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nf-core-bot
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28045430d1
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Template update for nf-core/tools version 2.5.1
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2022-09-01 13:34:04 +00:00 |
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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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