Moritz E. Beber
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5f3dbd28de
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fix: patch inputs to correspond to previous version
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2022-10-05 13:51:15 +02:00 |
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Moritz E. Beber
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180cac0395
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fix: adapt to new samtools/view input
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2022-10-05 13:49:35 +02:00 |
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Moritz E. Beber
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f5af9fd939
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fix: adjust import paths to re-organization
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2022-10-05 13:40:43 +02:00 |
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Moritz E. Beber
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b407fbcdce
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chore: force update all modules
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2022-10-05 12:24:18 +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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James A. Fellows Yates
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3ca9058b9c
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Merge pull request #133 from rafalstepien/add-pep-support
Add working version of PEP-nf-core integration
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2022-09-30 10:21:15 +02:00 |
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James A. Fellows Yates
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44146b8fe3
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Apply suggestions from code review
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2022-09-30 08:34:53 +02:00 |
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James A. Fellows Yates
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8b559fba86
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Pin version to get NXF to download correctly
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2022-09-29 13:31:02 -04:00 |
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Rafal Stepien
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04d28e6520
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Merge branch 'nf-core-add-pep-support' into add-pep-support
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2022-09-28 14:51:38 -04:00 |
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Rafal Stepien
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00aa94a403
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Merge branch 'add-pep-support' of github.com:nf-core/taxprofiler into nf-core-add-pep-support
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2022-09-28 14:51:13 -04:00 |
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Rafal Stepien
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bfd260e9c8
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Update workflows/taxprofiler.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-09-28 12:40:43 -04:00 |
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James Fellows Yates
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87edc4569c
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Move to a function
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2022-09-27 15:46:17 +02:00 |
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James Fellows Yates
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43a8aa4405
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Remove detect_reads.py and replace remaining checks with nextflow code instead
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2022-09-27 15:32:51 +02:00 |
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Rafal Stepien
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1584d6fc51
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Update workflows/taxprofiler.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-09-19 10:43:04 -04:00 |
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Rafal Stepien
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0ccbf50938
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Update nextflow_schema.json
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-09-19 09:49:37 -04:00 |
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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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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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James A. Fellows Yates
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187946ec80
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Merge pull request #136 from nf-core/metaphlan3/mergemetaphlantables
Add MetaPhlAn3 per-database multi-sample taxon tables
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2022-09-19 13:45:50 +02:00 |
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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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James A. Fellows Yates
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016efcb807
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Merge branch 'dev' into metaphlan3/mergemetaphlantables
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2022-09-16 16:02:38 +02:00 |
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James A. Fellows Yates
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a2a9f458ec
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Merge pull request #137 from nf-core/motus-merge-meta
Standardise mOTUs table merge
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2022-09-16 16:01:38 +02:00 |
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James A. Fellows Yates
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f43c54317c
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Update subworkflows/local/standardisation_profiles.nf
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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2022-09-16 15:20:47 +02:00 |
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James Fellows Yates
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63b3cc678f
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Merge branch 'motus-merge-meta' of github.com:nf-core/taxprofiler into motus-merge-meta
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2022-09-16 10:25:28 +02:00 |
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James Fellows Yates
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c5cc21d29e
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Update motus merge module to remove unused channel
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2022-09-16 10:25:24 +02:00 |
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James A. Fellows Yates
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2c83b367a7
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Apply suggestions from code review
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2022-09-16 09:28:42 +02:00 |
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James Fellows Yates
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4e7857e2ed
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Standardise mOTUs table merge
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2022-09-16 08:36:34 +02:00 |
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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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James A. Fellows Yates
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cdb21d17b3
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Merge branch 'dev' into metaphlan3/mergemetaphlantables
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2022-09-15 13:08:57 +02:00 |
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James A. Fellows Yates
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d9795a4fdc
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Merge pull request #130 from nf-core/krakentools/combinekreports
Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU
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2022-09-15 13:00:07 +02:00 |
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James Fellows Yates
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19a195ed14
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Append profiler to resulting file
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2022-09-15 12:30:39 +02:00 |
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James Fellows Yates
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21ae9d85c3
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Ensure merge metaphlan3 tables happens on per database basis
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2022-09-15 12:29:54 +02:00 |
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James A. Fellows Yates
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cd83c04c98
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Merge pull request #135 from nf-core/dev-warning
Update README.md
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2022-09-15 08:30:41 +02:00 |
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James A. Fellows Yates
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23a33a63cc
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Update README.md
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2022-09-15 08:11:37 +02:00 |
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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 A. Fellows Yates
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5414ae2e55
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Apply suggestions from code review
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2022-09-14 11:20:40 +02:00 |
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James Fellows Yates
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abbbf9c7ab
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Update to use tar module compatible for our test databases
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2022-09-14 11:16:28 +02:00 |
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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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James Fellows Yates
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05e9d92444
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Add centrigue kreports
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2022-09-13 16:47:19 +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 Fellows Yates
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c8dbf5be47
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Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU
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2022-09-13 15:47:28 +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 Fellows Yates
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a764bc4807
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Start works - need updated module though t have meta
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2022-09-09 13:57:06 +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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