James Fellows Yates
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fa70a413cb
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Use finally working filtlong module
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2022-05-31 21:12:09 +02:00 |
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James Fellows Yates
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16ec5bf74a
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Update parameter names
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2022-05-31 20:11:19 +02:00 |
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James Fellows Yates
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792e2d019b
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Fix merge error in schema
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2022-05-31 13:06:48 +02:00 |
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James Fellows Yates
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310ac6b450
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Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong
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2022-05-31 13:05:52 +02:00 |
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James A. Fellows Yates
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ba75685550
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Merge pull request #81 from nf-core/nf-core-template-merge-2.4
Important! Template update for nf-core/tools v2.4
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2022-05-19 11:00:48 +01:00 |
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Moritz E. Beber
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a9fbe47992
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Merge branch 'dev' into nf-core-template-merge-2.4
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2022-05-19 08:42:28 +02:00 |
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nf-core-bot
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a560492353
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Template update for nf-core/tools version 2.4
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2022-05-16 10:22:38 +00:00 |
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James A. Fellows Yates
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63d9cbbdfd
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Merge pull request #80 from nf-core/activate-pipeline-specific-profiles
Activate institutional specific profiles
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2022-05-12 11:00:49 +02:00 |
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James A. Fellows Yates
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aca7bc439d
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Update nextflow.config
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2022-05-12 08:08:14 +01:00 |
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James A. Fellows Yates
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fd71b71929
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Merge pull request #79 from nf-core/fastp-complexity
Add FASTP complexity option
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2022-05-07 14:05:32 +02:00 |
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James A. Fellows Yates
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d67543503b
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-05-07 13:15:21 +02:00 |
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James Fellows Yates
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3fa2181f49
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Fix prinseq tool selection
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2022-05-07 06:15:15 +02:00 |
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James Fellows Yates
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0f651873dd
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Linting
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2022-05-07 06:12:24 +02:00 |
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James Fellows Yates
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47a5ae0cff
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Add FASTP complexity option
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2022-05-07 06:09:05 +02:00 |
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James A. Fellows Yates
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e7b54801ed
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Merge pull request #75 from nf-core/improve-error-message
Only create profiler input channels when profiler activated
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2022-05-06 11:51:33 +02:00 |
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Lauri Mesilaakso
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e52a40cc9d
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Merge pull request #77 from genomic-medicine-sweden/add_nanopore_host_reads_removal_with_minimap2
Add nanopore host reads removal with minimap2
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2022-05-06 12:29:17 +03:00 |
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Lauri Mesilaakso
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02517733aa
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Update docs/usage.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-05-06 10:40:59 +02:00 |
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Lauri Mesilaakso
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b0faeedc60
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Update workflows/taxprofiler.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-05-06 08:20:31 +02:00 |
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ljmesi
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e3e55f57c2
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Fix alignment
Just made this change to see if the CI tests would fail again or if the
failure was just a one of thing.
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2022-05-05 14:02:24 +02:00 |
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ljmesi
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6618e8cac6
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Change param to a more generic name
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2022-05-05 13:20:34 +02:00 |
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ljmesi
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557d31dfd2
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Add parameter for turning on longread host removal
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2022-05-05 13:19:10 +02:00 |
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ljmesi
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d94534e8ac
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Simplify params which control host removal publish
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2022-05-05 09:07:33 +02:00 |
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ljmesi
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5b7b214156
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Fix formatting with prettier
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2022-05-05 08:40:53 +02:00 |
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ljmesi
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59c7f5a5b1
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Update samtools/bam2fq
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2022-05-05 08:38:41 +02:00 |
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ljmesi
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f4abbe280a
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Fix back to nf-core modules version
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2022-05-03 12:56:49 +02:00 |
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ljmesi
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c833d4fd9a
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Fix issues found with prettier
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2022-05-03 11:42:05 +02:00 |
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ljmesi
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58d4dec70b
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Update samtools view
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2022-05-03 11:09:54 +02:00 |
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ljmesi
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17039ebc6b
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Fix type to boolean for flags
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2022-05-03 11:07:23 +02:00 |
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ljmesi
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4b2a3789cd
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Update default values for host removal parameters
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2022-05-03 11:03:48 +02:00 |
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ljmesi
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fa1c132635
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Update nextflow_schema
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2022-05-03 11:03:25 +02:00 |
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ljmesi
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afdebaf09a
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Remove own modification to a module
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2022-05-03 10:15:11 +02:00 |
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ljmesi
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5e6be52fab
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Implement hostremoval
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2022-05-03 09:34:27 +02:00 |
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ljmesi
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a821f748ee
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Add modules
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2022-05-03 09:28:46 +02:00 |
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James Fellows Yates
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d5049a34e4
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Add missing close bracket
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2022-05-01 07:28:29 +02:00 |
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James Fellows Yates
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4094706421
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Only create profiler input channels when profiler activate
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2022-05-01 07:24:58 +02:00 |
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James Fellows Yates
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031cb45934
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Add initial longread QC filtering - requires filtlong module update
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2022-05-01 07:18:14 +02:00 |
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James A. Fellows Yates
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2bae9d58ee
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Merge pull request #72 from nf-core/diamond
Add DIAMOND
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2022-04-30 20:28:28 +02:00 |
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James Fellows Yates
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0630fce3b5
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Tweak based on official DIAMOND test-data
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2022-04-30 08:11:40 +02:00 |
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James Fellows Yates
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a4a9b161d8
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Lintin
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2022-04-29 22:02:44 +02:00 |
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James Fellows Yates
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8126d16dee
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Add draft version of DIAMOND
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2022-04-29 21:59:42 +02:00 |
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Sofia Stamouli
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120f86e5c7
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Merge pull request #67 from genomic-medicine-sweden/classification_kaiju2table
Add kaiju2table to taxprofiler
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2022-04-26 16:11:47 +02:00 |
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Sofia Stamouli
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194b89e66a
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Prettier
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2022-04-26 12:53:39 +02:00 |
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Sofia Stamouli
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7afda265c5
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Enumerating taxon
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2022-04-26 11:27:18 +02:00 |
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Sofia Stamouli
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f4480feb9b
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Prettier
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2022-04-25 17:45:26 +02:00 |
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sofstam
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d082d67bcb
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Add kaiju2table to taxprofiler
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2022-04-25 17:36:29 +02:00 |
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James A. Fellows Yates
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bc84afe80d
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Merge pull request #66 from nf-core/versions-fix
Fix version reporting
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2022-04-25 16:38:28 +02:00 |
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Sofia Stamouli
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1c694145d4
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Merge pull request #65 from genomic-medicine-sweden/classification_kreport
Add centrifuge kreport in taxprofiler
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2022-04-25 10:14:43 +02:00 |
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Sofia Stamouli
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e3a613de00
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Prettier
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2022-04-25 09:32:25 +02:00 |
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Sofia Stamouli
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d8a5c793e2
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Remove parameter from nextflow_schema
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2022-04-25 09:29:43 +02:00 |
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Sofia Stamouli
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ba2479b95b
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Prettier
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2022-04-25 09:26:49 +02:00 |
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