Rafal Stepien
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e84b64f7e1
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Update modules/local/samplesheet_check.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-09-19 09:49:20 -04:00 |
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Rafal Stepien
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9349346864
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Remove --pep parameter and leave just --input
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2022-09-16 10:14:01 -04:00 |
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Rafal Stepien
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768f9980d8
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Add pep_input_base_dir to workflow. Just need to update modules
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2022-09-15 12:31:49 -04:00 |
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Rafal Stepien
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5f3eee9a4a
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Add working version of PEP-nf-core integration
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2022-09-14 14:28:48 -04:00 |
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Sofia Stamouli
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343a9e8d16
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Merge pull request #131 from nf-core/FAQs_README
Update usage.md
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2022-09-14 09:00:17 +02:00 |
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Sofia Stamouli
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ded6d7ab1f
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Update docs/usage.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-09-13 18:13:00 +02:00 |
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Sofia Stamouli
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0072c29a6f
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Update docs/usage.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-09-13 18:12:14 +02:00 |
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Sofia Stamouli
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c664508240
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Update usage.md
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2022-09-13 15:56:06 +02:00 |
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James A. Fellows Yates
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db688575f6
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Merge pull request #128 from nf-core/fastp-patch-removal
use proper working FASTP module
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2022-09-09 19:07:12 +02:00 |
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James A. Fellows Yates
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b28052f1ec
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Remove patch from modules.json
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2022-09-09 11:15:25 +02:00 |
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James Fellows Yates
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f087136ec9
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use proper working FASTP module
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2022-09-09 11:12:47 +02:00 |
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James A. Fellows Yates
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3fc7f1f0f8
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Merge pull request #127 from nf-core/module-update
Update all modules
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2022-09-08 16:23:44 +02:00 |
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James Fellows Yates
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60224e9149
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Patch fastp until I have an OK on the module update
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2022-09-08 14:25:23 +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 A. Fellows Yates
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74c164bbcd
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Merge pull request #126 from nf-core/kaiju2table-move
Kaiju2table move
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2022-09-08 13:21:27 +02:00 |
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James Fellows Yates
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fc26948950
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Fix MultiQC
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2022-09-08 12:49:38 +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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bbd8049ca1
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Remove duplicated multqic mixing
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2022-09-07 13:44:08 +02:00 |
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James A. Fellows Yates
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6f87c681fd
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Merge pull request #125 from nf-core/workflow-tube-map
Workflow tube map
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2022-09-07 12:52:38 +02:00 |
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James Fellows Yates
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832d981976
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Don't have per sample directory as unnecessary if file names are unique with the db in them
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2022-09-07 12:22:17 +02:00 |
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James Fellows Yates
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3a6536b149
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Add tube map properly
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2022-09-07 11:22:22 +02:00 |
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James Fellows Yates
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175be0075a
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Add tube map
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2022-09-07 11:22:06 +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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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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