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Pre tag #132

Merged
merged 986 commits into from
Sep 19, 2023
Merged

Pre tag #132

merged 986 commits into from
Sep 19, 2023

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DLBPointon
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Pre-release PR

Talking with @priyanka-surana , we only need to get testing up and running (+ zenodo) and then we are ready for release.

To get that sorted i've been told to rope you in @muffato

yumisims and others added 30 commits June 8, 2023 22:52
@yumisims
SELFCOMP done
271efd9
@yumisims
Update output.md
00ecf03
@yumisims
INSILICO_DIGEST
fba443c
@yumisims
insilico digest done
07d4b9a
@yumisims
Update README.md
f608142
@yumisims
Update CITATIONS.md
0bf16fb
@weaglesBio
Minor doc fixes from proofread
9627c8e
@yumisims
put back selfcomp and insilico digest
9fcf17c
@DLBPointon
Fixes for PR plus Pretext name change requested
03121bb
@DLBPointon
Fixes
8913aea
@yumisims @DLBPointon
Updates to busco modules
3da5935
@DLBPointon
Merge branch 'template_update' of https://github.com/sanger-tol/treeval…
c19c9ae 
… into template_update
@DLBPointon
Updated to remove hardcoded arg
52f2435
@DLBPointon
Updating comment
bb3be5f
@DLBPointon
Fixed version error
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@DLBPointon
Fixing version informatino and harshil alignments
1ff0d3b
@DLBPointon
Updates to module configs and now outputting .hic
ef26ea4
@DLBPointon
adding BWAMEM2_INDEX config
b756b38
@yumisims
changed extract busco gene
afa5496
@yumisims
Update get_busco_gene.sh
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@yumisims
Update ancestral_gene.nf
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@yumisims
Update assign_ancestral.nf
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@yumisims
Update extract_ancestral.nf
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@yumisims
Update extract_buscogene.nf
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@yumisims
Merge pull request #118 from sanger-tol/busco_gene
7244261 
Busco gene
@weaglesBio
Troubleshoot rapid workflow
32ab7cd
@DLBPointon
Updates
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@DLBPointon
Merge branch 'template_update' of https://github.com/sanger-tol/treeval…
dbe1204 
… into template_update
@DLBPointon
Fix for multiple input to merge
aa1a554
@DLBPointon
Fixes to resource allocation
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DLBPointon and others added 14 commits September 15, 2023 16:41
@DLBPointon
Update TreeValProject.groovy
e9dd94d 
Adding the Duration import and .toSeconds()
@DLBPointon @muffato
Update docs/usage.md
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Co-authored-by: Matthieu Muffato <[email protected]>
@DLBPointon @muffato
Update docs/genealignmentsynteny.md
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Co-authored-by: Matthieu Muffato <[email protected]>
@DLBPointon @muffato
Update docs/genealignmentsynteny.md
9751a45 
Co-authored-by: Matthieu Muffato <[email protected]>
@DLBPointon @muffato
Update docs/genealignmentsynteny.md
4b01035 
Co-authored-by: Matthieu Muffato <[email protected]>
@DLBPointon @muffato
Update docs/genealignmentsynteny.md
3190ff2 
Co-authored-by: Matthieu Muffato <[email protected]>
@DLBPointon @muffato
Update docs/genealignmentsynteny.md
d80bfa2 
Co-authored-by: Matthieu Muffato <[email protected]>
@DLBPointon @muffato
Update docs/pacbio.md
7c1b69e 
Co-authored-by: Matthieu Muffato <[email protected]>
@DLBPointon
Merge pull request #140 from sanger-tol/mm49_pre_tag
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Code suggestions
@DLBPointon @muffato
Update docs/genealignmentsynteny.md
506dcc1 
Co-authored-by: Matthieu Muffato <[email protected]>
@DLBPointon @muffato
Update docs/usage.md
20aef5b 
Co-authored-by: Matthieu Muffato <[email protected]>
@DLBPointon
Updates to documentation after feedback
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@DLBPointon
Updates to documentation after feedback
03d27bd
@DLBPointon
Prettier Linting
56d6a75
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Here are some suggestions about the documentation. See #140 for a couple of code suggestions.

Also, before merging dev into main I'd very much like to see how the documentation looks like on the pipelines website, especially the fact there are more files than just usage.md and output.md.

I've actioned everything now, merged your code suggestions, and tested everything.
Thanks for the help.

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Prettier failing due to odd number of underscores....

This leaves us with a file called `bTaeGut1_4.fasta` the genomic assembly of bTaeGut1_4 (the [Tree of Life ID](https://id.tol.sanger.ac.uk/) for this species) also known as _Taeniopygia guttata_, the Australian Zebrafinch.

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muffato commented Sep 15, 2023

Prettier failing due to odd number of underscores....

Try escaping the one inside the assembly names with \ ?

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Prettier failing due to odd number of underscores....

Try escaping the one inside the assembly names with \ ?

Fixed, escaping wouldn't work. It would get "corrected". I've instead put the assembly name inside of backticks. Which also signifies importance so win-win.

@DLBPointon DLBPointon requested a review from muffato September 18, 2023 13:51
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Update docs/usage.md
6328583 
Spelling Mistake caught by muffato

Co-authored-by: Matthieu Muffato <[email protected]>
@DLBPointon DLBPointon requested a review from muffato September 19, 2023 08:34
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muffato approved these changes Sep 19, 2023
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Good for me ! Great work everyone

@DLBPointon DLBPointon merged commit d68fea5 into dev Sep 19, 2023
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@DLBPointon DLBPointon deleted the pre-tag branch September 19, 2023 10:10
@muffato muffato added this to the Release 1 milestone Sep 25, 2023
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REMINDER: Add tutorial documents and scripts
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@DLBPointon @muffato @priyanka-surana @yumisims @weaglesBio