Sarah Griffiths
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e3b1967872
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Improve ref annotation transcript id version handling
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2024-02-19 10:29:04 +00:00 |
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Sarah Griffiths
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e30d3aec98
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DE_analysis params change input types to numeric
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2024-02-16 10:23:15 +00:00 |
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Neil Horner
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bb9acf55be
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Resolve CW-3468 "Incorrect ids"
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2024-02-13 08:48:21 +00:00 |
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Neil Horner
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d5b0cc6203
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JAFFAL resources
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2024-02-12 15:25:19 +00:00 |
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Sarah Griffiths
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1c67e3274e
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Seperate DE files required for the report and to be output to the user
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2024-02-09 21:45:22 +00:00 |
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Neil Horner
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fdb938a147
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Publish isoforms table
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2024-02-09 10:59:01 +00:00 |
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Sarah Griffiths
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1be77ba77f
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CW-3075 improve counts output files
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2024-02-02 10:38:50 +00:00 |
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Neil Horner
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92cb357edc
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Template updates 2024 01 12
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2024-01-16 11:48:09 +00:00 |
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Sarah Griffiths
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b870078142
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tag v0.4.2
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2023-11-17 10:06:36 +00:00 |
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Sarah Griffiths
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e1b2a08918
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control for sample sheet
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2023-10-25 10:41:08 +00:00 |
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Sam Nicholls
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bb99170130
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Template updates [CW-1564][CW-2303][CW-2855]
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2023-10-16 14:17:32 +00:00 |
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Sarah Griffiths
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f683d44411
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CW-2769 remove denovo
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2023-09-27 08:02:00 +00:00 |
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Sarah Griffiths
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fb718ac3f7
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Update file check_sample_sheet.py
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2023-09-01 16:03:19 +00:00 |
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Sarah Griffiths
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ab850ac67f
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tidy up DE outputs
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2023-08-10 10:05:11 +00:00 |
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Sarah Griffiths
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ec3c346fd8
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fix and test for files with no gene id in attributes
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2023-07-26 18:14:00 +00:00 |
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Sarah Griffiths
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a58d08b6c4
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template updates
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2023-07-25 08:33:01 +00:00 |
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Sarah Griffiths
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f86b74a494
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CW-2217 fix ordering of sample_ids
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2023-07-12 11:05:34 +00:00 |
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Sarah Griffiths
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df6c9a2a31
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CW-2313 remove condition sheet requirement
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2023-07-10 16:45:32 +00:00 |
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Sarah Griffiths
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d0e7fc4b26
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CW-2308 remove real path use
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2023-06-28 17:37:49 +00:00 |
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Sarah Griffiths
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9f449ae467
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CW-2188 add test for denovo plus warnings
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2023-06-14 13:21:27 +00:00 |
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Sarah Griffiths
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ab275b6440
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CW-1920-Annotation-file-types
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2023-05-31 20:48:35 +00:00 |
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Sarah Griffiths
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5df7e3c2cd
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template updates
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2023-05-09 10:09:33 +00:00 |
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Sarah Griffiths
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8053448d61
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CW-1882 CSV
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2023-04-04 11:54:35 +00:00 |
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Neil Horner
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d8d8a791af
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Glue
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2023-02-24 14:42:57 +00:00 |
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Sarah Griffiths
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43e746f0ea
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schema updates
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2022-12-01 21:05:01 +00:00 |
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Sarah Griffiths
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5477e721a2
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CW-1170 Fix failed to plot
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2022-11-16 20:11:44 +00:00 |
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Sarah Griffiths
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cd1f97de4e
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CW-1162 option to run DE without assembly transcriptome
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2022-11-16 12:16:38 +00:00 |
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Neil Horner
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e339446a8a
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Fix for when JAFFAL returns exit status 1 when no fusions are found
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2022-11-15 19:56:46 +00:00 |
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Sarah Griffiths
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a111cae834
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CW-1167: error if conditionsheet and sample sheet dont match
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2022-11-15 14:59:43 +00:00 |
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Sarah Griffiths
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0758f4ab51
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demo data de
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2022-11-08 18:07:44 +00:00 |
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Neil Horner
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d8834b7573
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Verison bump
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2022-08-24 11:38:20 +01:00 |
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Sarah Griffiths
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c6b6121491
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CW-649
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2022-08-23 19:15:46 +00:00 |
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Neil Horner
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d477a747e6
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Switch isoform table thresholding to just displaying to n rows based on coverage
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2022-08-08 13:48:15 +00:00 |
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Neil Horner
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f481daad09
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Move pychopper report up to qc section
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2022-08-04 15:46:55 +00:00 |
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Neil Horner
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e63cc73b6c
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Fusions
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2022-08-01 19:07:20 +00:00 |
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Neil Horner
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956c80573a
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Fusions
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2022-08-01 12:01:01 +00:00 |
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Neil Horner
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d97e84cdc1
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Epi2melabs pychopper
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2022-06-01 12:08:00 +00:00 |
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Neil Horner
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3b69e64c4f
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Github issues
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2022-04-11 15:08:47 +00:00 |
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Neil Horner
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b4fac77b11
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Merge branch 'gh#8' into 'dev'
Empty dataframe bug
Closes CW-603
See merge request epi2melabs/workflow-containers/wf-isoforms!49
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2022-04-07 12:57:38 +00:00 |
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Neil Horner
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39f478ceef
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Empty dataframe bug
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2022-04-07 12:57:38 +00:00 |
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Neil Horner
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07275010c0
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Fnames
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2022-04-06 09:45:25 +00:00 |
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Neil Horner
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c2a0f8dc21
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Re-add ability to do direct RNA
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2022-04-05 18:04:16 +00:00 |
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Neil Horner
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4d91b738e1
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Post cw460
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2022-03-02 14:15:39 +00:00 |
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Neil Horner
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03b8ba51f6
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Denovo bug fixes
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2022-03-02 11:34:21 +00:00 |
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Neil Horner
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7e33eb2c3b
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Moved fiterable table into aplanat and general tidy up
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2022-02-28 14:17:46 +00:00 |
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Neil Horner
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5dfbb0f38a
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Merge de novo pipeline
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2022-01-26 15:54:55 +00:00 |
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Neil Horner
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458ac5d274
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Initial port of ref-isoforms to Nextflow
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2021-12-08 14:34:07 +00:00 |
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Karhide
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ca5111b287
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Add params table in report and process
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2021-07-29 12:32:19 +01:00 |
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Chris Wright
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635b18121b
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Fix typos
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2021-07-23 17:02:03 +01:00 |
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Chris Wright
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b61a1c0f5f
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Update version reporting
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2021-07-23 16:49:32 +01:00 |
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Chris Wright
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2a1ff88cc7
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add fastqingress module
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2021-07-12 21:15:03 +01:00 |
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Chris Wright
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c65c752277
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Add version report
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2021-04-29 14:52:21 +01:00 |
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Chris Wright
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d1901bb16f
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rename report
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2021-03-23 16:18:53 +00:00 |
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Chris Wright
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e8e584d451
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Set fastq option straight
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2021-03-19 11:22:10 +00:00 |
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Chris Wright
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3f99c88a9d
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Clean up bin
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2021-03-17 11:24:07 +00:00 |
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Chris Wright
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ed1fc2c9fd
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Add larger test data and sample report
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2021-03-01 11:44:41 +00:00 |
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Chris Wright
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5c60ad6779
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Backport additions from wf-artic
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2021-02-24 17:45:39 +00:00 |
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