James Fellows Yates
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56bae85755
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Remove necessity of patch
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2022-10-11 12:38:18 +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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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 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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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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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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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 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 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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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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05e9d92444
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Add centrigue kreports
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2022-09-13 16:47:19 +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 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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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 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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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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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 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 Fellows Yates
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d19a473c59
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Merge branch 'filtlong-in-tests' into json-schema
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2022-08-30 14:33:19 +02:00 |
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James Fellows Yates
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3f8f32cba8
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Make longread quality ftilering opt out
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2022-08-30 14:08:05 +02:00 |
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James Fellows Yates
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2cc07183a0
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Standardise QC parameter system and turn on both porechop/filtlong in tests
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2022-08-30 13:58:58 +02:00 |
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James Fellows Yates
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d4af88e3ff
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Make kaiju parameter clearer for documentation purpses and update documentation
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2022-08-25 15:50:28 +02:00 |
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James A. Fellows Yates
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de70b0a01d
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Merge pull request #109 from nf-core/centrifuge_mqc
Trying to get Centrifuge output into MQC
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2022-07-29 13:36:25 +02:00 |
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James A. Fellows Yates
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f48b22d615
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Apply suggestions from code review
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2022-07-29 09:52:49 +02:00 |
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James Fellows Yates
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873a13e028
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Merge remote-tracking branch 'origin/dev' into porechop-log
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2022-07-29 09:51:34 +02:00 |
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Mahwash Jamy
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49487593e2
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Merge branch 'nf-core:dev' into diamond-update
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2022-07-28 15:48:59 +02:00 |
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sofstam
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cecbb41f88
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Update centrifuge/kreport
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2022-07-27 14:42:35 +02:00 |
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James A. Fellows Yates
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9d2be68fb8
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Merge branch 'dev' into centrifuge_mqc
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2022-07-26 18:01:30 +00:00 |
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James A. Fellows Yates
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1ef0975736
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Merge branch 'dev' into porechop-log
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2022-07-26 18:00:28 +00:00 |
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James A. Fellows Yates
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3054dea7c2
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Get multiqc input working
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2022-07-26 08:41:06 +00:00 |
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James A. Fellows Yates
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e76b299705
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Start working getting kraken and centrifuge working in MQC
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2022-07-26 08:18:54 +00:00 |
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James Fellows Yates
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139cf0d6aa
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Fix
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2022-07-26 10:12:33 +02:00 |
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James A. Fellows Yates
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64f01fcfe0
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Merge branch 'dev' into porechop-log
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2022-07-20 14:05:23 +02:00 |
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James Fellows Yates
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255afee4c7
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Re-add the collects
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2022-07-19 17:10:10 +02:00 |
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Mahwash Jamy
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811ded38af
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Update subworkflows/local/profiling.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-07-19 16:44:48 +02:00 |
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Sofia Stamouli
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237e9aa623
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Update longread_preprocessing.nf
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2022-07-19 16:44:08 +02:00 |
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James A. Fellows Yates
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8d7ddb5847
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Apply suggestions from code review
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2022-07-19 16:30:13 +02:00 |
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mjamy
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c4c82212e1
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incorporate diamond log file into multiqc channel
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2022-07-19 14:12:16 +02:00 |
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sofstam
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171258d545
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Fix typos
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2022-07-19 14:07:13 +02:00 |
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sofstam
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25bc01f9c4
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Fix typos
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2022-07-19 14:04:49 +02:00 |
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sofstam
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8147dba0b4
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Fix typos
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2022-07-19 14:03:10 +02:00 |
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sofstam
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526ed79763
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Fix filtlong logs
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2022-07-19 14:01:11 +02:00 |
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sofstam
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1ba6a08135
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Seperate multiqc for filtlong
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2022-07-19 13:53:29 +02:00 |
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James Fellows Yates
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33a5402b25
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Add emitting porechop logs to multiqc and fix collection of others
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2022-07-19 13:50:39 +02:00 |
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sofstam
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3f5fa8cc7a
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Merge branch 'dev' into update_filtlong
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2022-07-19 13:50:28 +02:00 |
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