James A. Fellows Yates
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bb3c49389f
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Merge pull request #240 from nf-core/move-kaiju2table
Move kaiju2table to profiling
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2023-02-16 15:03:59 +01:00 |
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James Fellows Yates
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7dfcdd015b
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Re-add the 'native' combined kaiju output
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2023-02-16 14:02:13 +01:00 |
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James A. Fellows Yates
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4e818efe6d
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Update docs/output.md
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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2023-02-16 13:45:04 +01:00 |
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James Fellows Yates
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79b4db9a34
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Move kaiju2table to profiling
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2023-02-16 13:39:05 +01:00 |
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James A. Fellows Yates
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21d9135b14
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Merge pull request #238 from nf-core/process-optmisations
Resource optimisation
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2023-02-09 15:41:30 +01:00 |
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James Fellows Yates
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ce1118930d
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Resource optimisation
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2023-02-09 13:33:39 +01:00 |
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James Fellows Yates
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cc7d219267
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Revert "optimisation for single-cpu processes"
This reverts commit a731669b8e.
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2023-02-09 13:32:29 +01:00 |
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James Fellows Yates
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a731669b8e
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optimisation for single-cpu processes
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2023-02-09 13:31:57 +01:00 |
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James A. Fellows Yates
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45ac6fedc2
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Merge pull request #237 from nf-core/bracken-params
Support Kraken and Bracken db_params in database sheet
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2023-02-09 10:59:27 +01:00 |
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James A. Fellows Yates
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70eb84b8d5
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2023-02-09 08:01:52 +01:00 |
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James Fellows Yates
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b3837cce5b
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Relax strictness so can supply empty db_params but block if only single parameter with out ;
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2023-02-08 15:44:37 +01:00 |
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James Fellows Yates
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fe3d42ffd7
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Make bracken db_params be a semi-colon separate list to allow kraken and bracken parameters
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2023-02-08 13:34:36 +01:00 |
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James A. Fellows Yates
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31d05d1994
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Merge pull request #236 from nf-core/mapped-bam-fixes
Fix exporting of mapped/unmapped reads for consistency across both short and long reads
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2023-02-07 18:42:18 +01:00 |
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James Fellows Yates
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18886c0cbc
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Start trying a different method with maps in profiling
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2023-02-07 15:51:25 +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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de5bdc36c5
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Merge pull request #230 from genomic-medicine-sweden/documentation
Add documentation
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2023-02-03 16:34:09 +01:00 |
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sofstam
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4123e06981
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Apply last review suggestions
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2023-02-03 15:54:29 +01:00 |
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sofstam
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3e2b181182
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Apply review suggestions
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2023-02-03 15:42:45 +01:00 |
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Sofia Stamouli
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ffc884b542
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Merge branch 'nf-core:dev' into documentation
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2023-02-03 15:22:51 +01:00 |
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James A. Fellows Yates
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2b40d809d8
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Merge pull request #231 from nf-core/docs-t [skip ci]
Add warning about database parameters [skip ci]
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2023-02-03 10:14:38 +01:00 |
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James A. Fellows Yates
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b4f88a29ce
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Update docs/usage.md [skip ci]
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2023-02-03 09:46:01 +01:00 |
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James A. Fellows Yates
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11a8624b39
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Add warning about database parameters [skip ci]
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2023-02-03 09:42:20 +01:00 |
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sofstam
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5363274867
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Add some last documentation
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2023-02-02 13:58:48 +01:00 |
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James A. Fellows Yates
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2e925e5b11
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Merge pull request #229 from nf-core/full-test-profile-docs
Add full test data and documentation of the test data
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2023-02-02 13:10:39 +01:00 |
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James Fellows Yates
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7ce55a99e8
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Fix linting
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2023-02-02 13:08:16 +01:00 |
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James A. Fellows Yates
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c4e366d47d
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Add full test data and documentation of the test data
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2023-02-02 11:59:26 +01:00 |
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James A. Fellows Yates
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a6b4e3c4d4
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Merge pull request #225 from nf-core/output-docs-imporvements
Output Formatting tweaks
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2023-01-31 13:25:07 +01:00 |
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James Fellows Yates
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932dc12fb1
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Add list of expected tools in MultiQC report [skip ci]
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2023-01-31 13:09:53 +01:00 |
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James Fellows Yates
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52907dcc26
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Prettier
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2023-01-31 13:07:07 +01:00 |
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James A. Fellows Yates
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d49344cefd
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Merge pull request #228 from nf-core/bt2-error
Fix channel structure when supplying own host bt2 index
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2023-01-31 13:03:53 +01:00 |
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James Fellows Yates
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225773000f
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Fix channel structure when supplying own host bt2 index
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2023-01-31 12:00:48 +01:00 |
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James A. Fellows Yates
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43a503096e
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Merge pull request #227 from nf-core/mqc-update [skip ci]
Tweak MultiQC config [skip ci]
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2023-01-31 11:11:52 +01:00 |
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James Fellows Yates
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01fca90496
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Tweak MultiQC config [skip ci]
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2023-01-31 11:08:46 +01:00 |
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James A. Fellows Yates
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b4d01ac226
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Formatting tweaks
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2023-01-31 10:23:36 +01:00 |
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James A. Fellows Yates
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f47c294931
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Merge pull request #186 from genomic-medicine-sweden/update_output
Start the documentation of output.md
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2023-01-31 09:58:54 +01:00 |
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sofstam
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366745bdbe
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Prettier in usage
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2023-01-31 09:38:43 +01:00 |
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sofstam
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5b738ad353
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Review + prettier
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2023-01-31 09:35:40 +01:00 |
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James A. Fellows Yates
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1d7da61801
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Merge pull request #223 from nf-core/multiqc-tweaks
MultiQC Tweaks after full-test experiments
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2023-01-30 11:25:28 +01:00 |
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sofstam
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0edef9ea57
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Review suggestions + prettier
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2023-01-30 11:16:18 +01:00 |
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sofstam
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bc2876228c
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Apply review suggestions
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2023-01-25 15:11:43 +01:00 |
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James Fellows Yates
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a77a437313
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Triple patch combo!
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2023-01-25 15:02:02 +01:00 |
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James Fellows Yates
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f63cec3473
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Actually patch the patch
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2023-01-25 14:58:19 +01:00 |
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James Fellows Yates
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d761edb615
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Patch the patch
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2023-01-25 14:55:57 +01:00 |
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James A. Fellows Yates
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47efd193cb
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Merge pull request #219 from nf-core/allow-targz-motus [skip ci]
Allow all tool's databases to be provided as `.tar.gz` files
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2023-01-25 13:48:43 +01:00 |
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James A. Fellows Yates
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2cbb56194a
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Merge pull request #224 from nf-core/revert-metaphlan-nanopore-filter [skip ci]
Remove metaphlan3 nanopore filter as _sometimes_ it can work
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2023-01-25 13:48:29 +01:00 |
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James A. Fellows Yates
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098ec087c9
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Merge pull request #217 from nf-core/combine-kreports-fix [skip ci]
Dont fail on divide by 0 errors on centrifuge
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2023-01-25 13:48:06 +01:00 |
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sofstam
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4f8ac72e1f
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Add description of each tool
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2023-01-25 13:25:33 +01:00 |
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Sofia Stamouli
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5d12785ca4
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Merge branch 'nf-core:dev' into update_output
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2023-01-25 09:47:30 +01:00 |
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James A. Fellows Yates
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4289e1f901
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Remove metaphlan3 nanopore filter as _sometimes_ it can work
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2023-01-24 15:42:14 +01:00 |
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James Fellows Yates
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7843665544
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Link rather than mv
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2023-01-24 15:32:49 +01:00 |
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