sofstam
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1347f27c11
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Update changelog after release
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2023-03-13 12:21:37 +01:00 |
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James Fellows Yates
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98bc6910d5
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Update authors and remove left over comment
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2023-03-07 11:47:54 +01:00 |
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James A. Fellows Yates
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f0f89eb082
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Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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2023-03-03 14:58:21 +01:00 |
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James A. Fellows Yates
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c66c67524c
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Update nextflow.config
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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2023-03-03 13:33:41 +01:00 |
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James A. Fellows Yates
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6c2ce4a1c9
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Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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2023-03-03 08:37:31 +01:00 |
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James Fellows Yates
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aedf0b34de
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Bump version for release
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2023-03-02 13:51:28 +01:00 |
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James Fellows Yates
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5c549e5ce3
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Remove TODOs and references to under development
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2023-03-02 13:49:03 +01:00 |
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Sofia Stamouli
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69430ef851
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Update nextflow.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2023-02-27 11:02:55 +01:00 |
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sofstam
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2f0c68a833
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Last review suggestions
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2023-02-27 10:15:42 +01:00 |
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sofstam
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e18e68faa5
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Apply review suggestion
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2023-02-24 15:50:24 +01:00 |
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sofstam
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5dc3cbc278
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Rename taxonomy argument
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2023-02-24 13:04:38 +01:00 |
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sofstam
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5a6fcf1f42
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Update taxpasta/merge to version 0.2.0 and add taxonomy argument
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2023-02-24 11:44:07 +01:00 |
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sofstam
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04bc978ef6
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Remove taxonomy parameter from taxpasta
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2023-02-20 11:56:06 +01:00 |
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sofstam
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f0aa89cb87
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Rename taxpasta parameters and remove samplesheet parameter
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2023-02-17 14:47:29 +01:00 |
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sofstam
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25d44c955e
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Merge dev into add_taxpasta_merge
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2023-02-16 15:16:05 +01:00 |
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sofstam
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de6a4214ef
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Add taxpasta_merge to taxprofiler
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2023-02-16 14:29:52 +01:00 |
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James Fellows Yates
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059cd17114
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Fix exporting of mapped/unmapped reads for consistency across both short and long reads
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2023-02-07 11:43:40 +01:00 |
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James A. Fellows Yates
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1279437aa1
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Apply suggestions from code review
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2022-12-20 21:48:08 +01:00 |
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Sofia Stamouli
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d691b89727
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Merge branch 'dev' into nf-core-template-merge-2.7.2
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2022-12-20 15:14:41 +01:00 |
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nf-core-bot
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ab591e01ff
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Template update for nf-core/tools version 2.7.2
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2022-12-19 12:10:58 +00:00 |
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James Fellows Yates
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4b68e95770
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Revert PEP validation back to python samplesheet check
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2022-12-12 08:49:13 +01:00 |
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James Fellows Yates
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1ccd0a0767
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Merge branch 'dev' into nf-core-template-merge-2.7.1
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2022-12-09 10:16:17 +01:00 |
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nf-core-bot
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36f3b5723b
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Template update for nf-core/tools version 2.7.1
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2022-12-08 13:18:23 +00:00 |
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James Fellows Yates
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3dba6405c5
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Sets correct default for --shortread_qc_mergepairs
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2022-12-06 11:47:16 +01:00 |
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Moritz E. Beber
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4529e7e545
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refactor: change parameter exclude unmerged to include
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2022-12-04 21:36:12 +01:00 |
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sofstam
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6d140c683a
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Merge branch 'dev' into update_motus
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2022-12-01 18:49:23 +01:00 |
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sofstam
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38a818fd17
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Apply review suggestions
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2022-12-01 13:42:21 +01:00 |
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sofstam
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e5bb627402
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Apply review suggestions
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2022-12-01 11:12:31 +01:00 |
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James Fellows Yates
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bc98f5b80f
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Separate KrakenUniq test run
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2022-12-01 10:37:14 +01:00 |
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James A. Fellows Yates
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4f6eb6fd75
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Merge pull request #153 from mjamy/add-krakenuniq-module
Add krakenuniq module
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2022-12-01 09:03:29 +01:00 |
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sofstam
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933b820c19
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Apply review suggestions
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2022-11-29 16:57:07 +01:00 |
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sofstam
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49af33f68e
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Include NCBI_id, read counts and mgc arguments in motus
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2022-11-29 11:07:29 +01:00 |
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James Fellows Yates
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c5e5696f84
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Fix parameter name
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2022-11-03 14:58:03 +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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James A. Fellows Yates
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1f31f88635
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Merge pull request #158 from nf-core/adapterremoval-fix
Fix adapterremoval adapter conflict and add optional adapter list file
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2022-11-03 11:36:14 +01:00 |
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James A. Fellows Yates
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62f45c8be7
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Update nextflow.config
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2022-11-03 10:03:27 +01:00 |
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Mahwash Jamy
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febcbfc057
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add missing parameters to nextflow.config
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2022-10-31 16:07:53 +00:00 |
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Moritz E. Beber
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bf89525bc2
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Merge pull request #146 from nf-core/feat-bracken
add Bracken to the profiling workflow
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2022-10-27 17:35:06 +02:00 |
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James A. Fellows Yates
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76a662ecc5
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Fix adapterremoval adapter conflict and add optional adapter list file
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2022-10-27 12:17:19 +00:00 |
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Moritz E. Beber
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60e369aa5c
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fix: set default run bracken to false
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2022-10-21 10:47:51 +02:00 |
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Sofia Stamouli
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511cb16a61
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Apply review suggestions
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2022-10-20 16:55:57 +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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fdb8a7f740
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Merge branch 'devel' into nf-core-template-merge-2.6
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2022-10-05 12:21:54 +02:00 |
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nf-core-bot
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51bacb00e6
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Template update for nf-core/tools version 2.6
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2022-10-05 03:30:53 +00:00 |
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Rafal Stepien
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5b6c18f0a2
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Update nextflow.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-09-19 09:49:28 -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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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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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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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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