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Many additions #48

Merged
merged 120 commits into from
Sep 11, 2024
Merged

Many additions #48

merged 120 commits into from
Sep 11, 2024

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DLBPointon
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Additions include:

  • create_btk_datasets
    • module, python scripts
  • merge_btk_datasets
    • module, python scripts
  • ASCC merge tables
    • module, python scripts
  • Trailing N's <-- Written by @eeaunin and this should have been attributed properly. Copy pasting is much quicker than merging from an old PR.
    • module, python script
  • Various fixes
  • Modularised module flag

DLBPointon and others added 30 commits April 5, 2024 12:39
@DLBPointon
initial work on the merge modules
9513796
@DLBPointon
Updates to the create_btk_dataset process
3d4dbc7
@DLBPointon
Updates to the create_btk_dataset process
e040d3e
@DLBPointon
Adding Diamond Blast subworkflow
b3fc8f2
@DLBPointon
Added the UNIPROT diamond blast subworkflow
992fe3f
@DLBPointon
Typo
5d28b47
@DLBPointon
additions to scripts and a rewrite
951c248
@DLBPointon
Adding and updating modules
c45bc2c
@DLBPointon
Adding more modules
d07cb6b
@DLBPointon
Updating the modules conf for the diamond blastx
3c5102c
@DLBPointon
updates to modules
62f528e
@DLBPointon
Update to config
ee1bbdc
@DLBPointon
Addition of the V2 python scripts
c9dab6b
@DLBPointon
Modifications for malformed channels
c2c76c3
@DLBPointon
Updated
13eabcc
@DLBPointon
Updated
947b1c7
@DLBPointon
Addition of a V2 python script
c5cd5f7
@DLBPointon
updates for merge BTK datasets
b0903e4
@DLBPointon
Remove ls -lh and unnecessary args
c09a852
@DLBPointon
Addition of the trimNs subworkflow
ddc627d 
Co-authored-by: eeanuin <[email protected]>
@DLBPointon
Addition of the trimNs subworkflow
581bb91 
Co-authored-by: eeanuin <[email protected]>
@DLBPointon
Addition of the trimNs subworkflow
001b2f7 
Co-authored-by: eeanuin <[email protected]>
@DLBPointon
Addition of the trimNs subworkflow
1c086f7 
Co-authored-by: eeanuin <[email protected]>
@DLBPointon
Addition of the ascc merge tables module
3a28d35
@DLBPointon
module which was missing from the diamond subworkflow, required to ge…
645df15 
…nerate the hits file
@DLBPointon
Updates to the modules
e71c6d5
@DLBPointon
Updating modules config
98a8bc1
@DLBPointon
Addition of a new module to generate the hits file
3554bbf
@DLBPointon
Addition of re-written scripts
dcc82ba
@DLBPointon
Addition of re-written scripts
90359a3
eeaunin and others added 17 commits August 7, 2024 13:01
ea10 edits to dp24_btk_datasets_branch
39393ef
07.08.2024 edits
afc73ed
ran linting with black
e3b8db9
@DLBPointon
Updating the version of BTK, spelling and bug fixes
6d6b6fa
@DLBPointon
Merge branch 'dp24_btk_datasets' into dp24_btk_datasets_ea10_edits2
7e7370b
@DLBPointon
Merge pull request #55 from sanger-tol/dp24_btk_datasets_ea10_edits2
748b3ca 
Edits to the dp24_btk_datasets branch
@DLBPointon
Addition of new scripts to filter and double check data
b1e214b
@DLBPointon
Adding new scripts for filtering and double checking data #56
a599125
@DLBPointon
Updates for #56
aeb7097
@DLBPointon
Updates for #56
7405a9b
@DLBPointon
Updates closes #56 and additions to the output.md file
6008006
@DLBPointon
Prettier linting
00b375a
@DLBPointon
Update to the sanger-tol module to remove the yaml flag which is now …
646ae91 
…depreciated
@DLBPointon
closes #57 filters the output to that directly needed for analysis
124a50a
@DLBPointon
Addition of 2/3 indicator files needed for integration into the curre…
1db6429 
…nt sanger automation workflows
@DLBPointon
Addition of 2/3 indicator files needed for integration into the curre…
0bbd384 
…nt sanger automation workflows
@DLBPointon
Addition of indicator files, these are saved to the main outdir
dfdbb8d
This was linked to issues Aug 9, 2024
Layer 3 - CSV table of average per Phylum #16
Closed
Add new scripts to ASCC for 0.5.0 #56
Closed
Trimming down output #57
Closed
Layer 1 - BUSCO-based BTK #2
Closed
@DLBPointon DLBPointon merged commit f51e910 into dev Sep 11, 2024
6 checks passed
@DLBPointon DLBPointon deleted the dp24_btk_datasets branch September 11, 2024 05:53
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@eeaunin eeaunin eeaunin approved these changes

@weaglesBio weaglesBio Awaiting requested review from weaglesBio

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@DLBPointon @eeaunin