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 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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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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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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James A. Fellows Yates
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c215ed5607
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Merge branch 'dev' into motus/merge
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2022-07-15 10:52:42 +02:00 |
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James A. Fellows Yates
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cc3967a3fd
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Apply suggestions from code review
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2022-07-15 10:51:41 +02:00 |
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James Fellows Yates
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31119f83c2
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Send to MQC only the log file not the meta
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2022-07-13 14:29:47 +02:00 |
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James Fellows Yates
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13280e2468
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Fix .empty
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2022-07-13 12:44:44 +02:00 |
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James Fellows Yates
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eaa69b65d8
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Update mOTUs profile module and mix log for multiqc
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2022-07-13 12:38:30 +02:00 |
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James Fellows Yates
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c22946cfab
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Fix motu versions not being exported if not run
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2022-07-13 12:36:29 +02:00 |
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James Fellows Yates
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a0ee82bf43
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Add motus/merge and biom support
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2022-07-12 11:39:26 +02:00 |
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James A. Fellows Yates
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26e31c782d
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Merge branch 'dev' into motus
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2022-07-04 13:14:42 +02:00 |
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6673ccf8d8
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Update channel assignment alignment in profiling subworkflow
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-06-28 09:00:43 -05:00 |
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4de43040a3
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Switch to using raw classifications for Kaiju2Krona
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2022-06-28 09:00:41 -05:00 |
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James Fellows Yates
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e0ad49ebc9
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Fix metadata manipulaton for malt
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2022-06-10 19:33:37 +02:00 |
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James A. Fellows Yates
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621b6a3d09
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Add comments about MALT id replacement and refactor for simplicity
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2022-06-10 11:27:51 +02:00 |
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James A. Fellows Yates
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ebdd5683b2
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Apply suggestions from code review
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2022-06-03 22:33:48 +02:00 |
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James Fellows Yates
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9462032d00
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Fix MALT save_alignemnts reads and some clean up
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2022-06-03 22:29:04 +02:00 |
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JIANHONG OU
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4b3216c1cb
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filter fasta inputs for mOTUs;
fix the typo for nopreprocessing in nextflow.config.
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2022-05-24 08:42:18 -04:00 |
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JIANHONG OU
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68d0cc00fa
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add motus profile.
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2022-05-23 08:05:06 -04:00 |
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James Fellows Yates
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87a1d80519
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Add working output for Kraken2/Centrifuge/DIAMOND
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2022-05-07 05:22:35 +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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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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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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James Fellows Yates
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06b38f3699
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Fix crash, add missing versions
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2022-04-23 08:36:01 +02:00 |
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sofstam
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c00ca1c2b8
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Add centrifuge kreport in taxprofiler
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2022-04-22 15:24:10 +02:00 |
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Sofia Stamouli
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e71e7b86a2
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Merge pull request #53 from genomic-medicine-sweden/classification_kaiju
Add kaiju/kaiju in taxprofiler
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2022-04-20 10:57:00 +02:00 |
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Sofia Stamouli
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236141f065
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Resolve conflicts with dev
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2022-04-20 10:17:10 +02:00 |
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James A. Fellows Yates
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571495c812
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Merge pull request #60 from nf-core/fasta-filtering
Adds filtering out of FASTA for tools that don't support it
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2022-04-20 10:11:17 +02:00 |
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James Fellows Yates
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9fd94b1389
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Switch to string interpolation
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2022-04-20 09:25:54 +02:00 |
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James Fellows Yates
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60d232d62c
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Revert "Update subworkflows/local/profiling.nf"
This reverts commit b7d0557ee0 .
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2022-04-20 09:23:38 +02:00 |
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James A. Fellows Yates
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b7d0557ee0
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Update subworkflows/local/profiling.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-04-20 09:15:45 +02:00 |
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James A. Fellows Yates
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87777a4289
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Update subworkflows/local/profiling.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-04-19 12:54:57 +02:00 |
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James A. Fellows Yates
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9f634805e4
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Update subworkflows/local/profiling.nf
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2022-04-18 07:31:44 +02:00 |
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James A. Fellows Yates
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9c3c8f1f4e
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Merge branch 'dev' into fasta-filtering
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2022-04-18 07:31:14 +02:00 |
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James Fellows Yates
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6307a9cf43
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Typos
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2022-04-18 07:28:09 +02:00 |
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James Fellows Yates
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491c2d8949
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Revert "Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages."
This reverts commit 564474cafe .
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2022-04-18 07:26:15 +02:00 |
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James Fellows Yates
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564474cafe
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Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages.
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2022-04-18 07:21:12 +02:00 |
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James Fellows Yates
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cc73cdd51d
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Add generation of taxon-table like output for MALT
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2022-04-16 07:42:30 +02:00 |
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James A. Fellows Yates
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6fecb3eeb7
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Merge pull request #54 from nf-core/dev
Get upstream changes
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2022-04-16 06:17:33 +02:00 |
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sofstam
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68ce5843a4
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Add kaiju in taxprofiler
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2022-04-13 18:51:56 +02:00 |
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James Fellows Yates
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de57340526
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Start work
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2022-04-13 11:49:35 +02:00 |
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James Fellows Yates
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a15c45b00c
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Put map in the rigt place
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2022-04-12 10:51:27 +02:00 |
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James Fellows Yates
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8d68914192
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Re-add operator name
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2022-04-12 10:47:44 +02:00 |
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James Fellows Yates
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26399718b2
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Re-add pairment attachment
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2022-04-12 10:46:03 +02:00 |
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James Fellows Yates
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2ef21c6ef3
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Fix input to profiling
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2022-04-12 10:14:05 +02:00 |
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James Fellows Yates
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9f221f84cc
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Only supply single input channel to profiling, as these are merged into single input channel at run_merging
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2022-04-12 10:12:17 +02:00 |
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